CINXE.COM

<!DOCTYPE html> <html lang="en" class="theme_DF no_contentMenu"><head> <meta name="viewport" content="width=device-width, initial-scale=1"> <base href="/"> <link rel="search" type="application/opensearchdescription+xml" title="PDBj Search" href="./pdbj_search.xml" /><script>window.fromStatic=true; window.newweb = {call: function(a,b,c) {setTimeout(function(){newweb.call(a,b,c);}, 100)}}; function importNewweb(a,b) {setTimeout(function() {importNewweb(a,b);}, 100);}</script><link rel="icon" type="image/png" sizes="16x16" href="./newweb/media/icons/favicon16.png"><link rel="icon" type="image/png" sizes="32x32" href="./newweb/media/icons/favicon32.png"><link rel="icon" type="image/png" sizes="64x64" href="./newweb/media/icons/favicon64.png"><link rel="icon" type="image/svg+xml" sizes="any" href="./newweb/media/icons/favicon.svg"><style data-module="core">:root.theme_oldDF{--COLOUR__MAIN:#9DCDC5;--COLOUR__MAIN_MILD:191,223,217;--COLOUR__MAIN_OPPOSITE:#C8323A;--COLOUR__MAIN_BORDER:#BFDFD9;--COLOUR__MAIN_SELECT:#9DCDC5;--COLOUR__MAIN_MILD_SELECT:#E1EFED;--COLOUR__SWITCH_1:#FFFFFF;--COLOUR__SWITCH_2:#F0F1F2;--COLOUR__SWITCH_3:#F5F5F5;--COLOUR__MAIN_ACCENT:#FFFFFF;--COLOUR__BG:#F8F8FC;--COLOUR__TXT:#000000}:root.theme_DF{--COLOUR__MAIN:#9DCDC5;--COLOUR__MAIN_MILD:157,205,173;--COLOUR__MAIN_OPPOSITE:#cd9da5;--COLOUR__MAIN_BORDER:#9dcdad;--COLOUR__MAIN_SELECT:#9DCDC5;--COLOUR__MAIN_MILD_SELECT:#e6f2f1;--COLOUR__SWITCH_1:#FFFFFF;--COLOUR__SWITCH_2:#F0F1F2;--COLOUR__SWITCH_3:#F5F5F5;--COLOUR__MAIN_ACCENT:#FFFFFF;--COLOUR__BG:#F8F8FC;--COLOUR__TXT:#000000}:root.theme_OB{--COLOUR__MAIN:#45A1DE;--COLOUR__MAIN_MILD:198,227,245;--COLOUR__MAIN_OPPOSITE:#C8323A;--COLOUR__MAIN_BORDER:#C6E3F5;--COLOUR__MAIN_SELECT:#45A1DE;--COLOUR__MAIN_MILD_SELECT:#E7F0FF;--COLOUR__SWITCH_1:#FFFFFF;--COLOUR__SWITCH_2:#F0F1F2;--COLOUR__SWITCH_3:#F5F5F5;--COLOUR__MAIN_ACCENT:#FFFFFF;--COLOUR__BG:#F8F8FC;--COLOUR__TXT:#000000}:root.theme_MS{--COLOUR__MAIN:#C0C0C0;--COLOUR__MAIN_MILD:217,217,217;--COLOUR__MAIN_OPPOSITE:#C8323A;--COLOUR__MAIN_BORDER:#BFBFBF;--COLOUR__MAIN_SELECT:#C0C0C0;--COLOUR__MAIN_MILD_SELECT:#FED6D2;--COLOUR__SWITCH_1:#FFFFFF;--COLOUR__SWITCH_2:#F0F1F2;--COLOUR__SWITCH_3:#F5F5F5;--COLOUR__MAIN_ACCENT:#EAEAEA;--COLOUR__BG:#F8F8FC;--COLOUR__TXT:#000000}:root.theme_PG{--COLOUR__MAIN:#C7F3A0;--COLOUR__MAIN_MILD:213,246,184;--COLOUR__MAIN_OPPOSITE:#C8323A;--COLOUR__MAIN_BORDER:#ACED73;--COLOUR__MAIN_SELECT:#C7F3A0;--COLOUR__MAIN_MILD_SELECT:#A1E887;--COLOUR__SWITCH_1:#FFFFFF;--COLOUR__SWITCH_2:#EAEAEA;--COLOUR__SWITCH_3:#F5F5F5;--COLOUR__MAIN_ACCENT:#FFFFFF;--COLOUR__BG:#F8F8FC;--COLOUR__TXT:#000000}:root.theme_PP{--COLOUR__MAIN:#FAE7CA;--COLOUR__MAIN_MILD:255,243,224;--COLOUR__MAIN_OPPOSITE:#C8323A;--COLOUR__MAIN_BORDER:#FFDEAD;--COLOUR__MAIN_SELECT:#FAE7CA;--COLOUR__MAIN_MILD_SELECT:#FFF3E0;--COLOUR__SWITCH_1:#FFFFFF;--COLOUR__SWITCH_2:#EAEAEA;--COLOUR__SWITCH_3:#F5F5F5;--COLOUR__MAIN_ACCENT:#FFFFFF;--COLOUR__BG:#F8F8FC;--COLOUR__TXT:#000000}:root.theme_GD{--COLOUR__MAIN:#F3E472;--COLOUR__MAIN_MILD:247,237,161;--COLOUR__MAIN_OPPOSITE:#C8323A;--COLOUR__MAIN_BORDER:#EFDB43;--COLOUR__MAIN_SELECT:#F3E472;--COLOUR__MAIN_MILD_SELECT:#F7EDA1;--COLOUR__SWITCH_1:#FFFFFF;--COLOUR__SWITCH_2:#EAEAEA;--COLOUR__SWITCH_3:#F5F5F5;--COLOUR__MAIN_ACCENT:#FFFFFF;--COLOUR__BG:#F8F8FC;--COLOUR__TXT:#000000}:root.theme_RD{--COLOUR__MAIN:#EB7647;--COLOUR__MAIN_MILD:242,169,140;--COLOUR__MAIN_OPPOSITE:#45A1DE;--COLOUR__MAIN_BORDER:#F2A98C;--COLOUR__MAIN_SELECT:#EB7647;--COLOUR__MAIN_MILD_SELECT:#F2A98C;--COLOUR__SWITCH_1:#FFFFFF;--COLOUR__SWITCH_2:#EAEAEA;--COLOUR__SWITCH_3:#F5F5F5;--COLOUR__MAIN_ACCENT:#FFFFFF;--COLOUR__BG:#F8F8FC;--COLOUR__TXT:#000000}:root.theme_DK{--COLOUR__MAIN:#404040;--COLOUR__MAIN_MILD:8,8,8;--COLOUR__MAIN_OPPOSITE:#cd9da5;--COLOUR__MAIN_BORDER:#303030;--COLOUR__MAIN_SELECT:#404040;--COLOUR__MAIN_MILD_SELECT:#190D0E;--COLOUR__SWITCH_1:#000000;--COLOUR__SWITCH_2:#0F0E0D;--COLOUR__SWITCH_3:#190D0E;--COLOUR__MAIN_ACCENT:#202020;--COLOUR__BG:#000000;--COLOUR__TXT:#FFFFFF}@media only screen and (min-width:75em){header{width:67%;left:16.5%}nav{width:15.25%;display:inline-block}#pageDIV>div{width:67%;left:16.5%}aside{position:absolute;right:-25%;top:0;width:22.8%;margin-right:1.1%}header>:first-child>:nth-child(4)>:nth-child(1){display:none}}@media only screen and (max-width:75em){nav{width:24%;display:inline-block}header{left:.5%}header:after{left:.5%}#pageDIV>div{left:.5%}}@media only screen and (min-width:40.001em){header{height:10.5em}nav{top:11.5em}#pageDIV>div{top:11.5em}aside{z-index:10}}@media only screen and (max-width:40em){aside{max-width:15em;margin:0 auto}}@media only screen and (min-width:40.001em) and (max-width:75em){header{width:74.5%}#pageDIV>div{width:74.5%}nav{width:25%;min-width:25em;display:none;z-index:999}aside{position:absolute;right:-34%;top:0;width:32%;margin-right:1.1%}}@media only screen and (max-width:40em){header{width:99%;left:.5%;height:8em}header:after{height:8em}#pageDIV>div{width:99%;left:.5%;top:9em}nav{top:9em;width:50%;display:none;z-index:999}header>:first-child>:nth-child(4)>:nth-child(1){display:inline-block}}@media only screen and (max-width:15em){nav{width:100%!important}}.no_contentMenu aside{visibility:hidden;opacity:0}@media only screen and (min-width:75em){.no_contentMenu header{width:82.5%}.no_contentMenu #pageDIV>div{width:82.5%}}@media only screen and (min-width:40.001em) and (max-width:75em){.no_contentMenu header{width:99%}.no_contentMenu #pageDIV>div{width:99%}}.minimalDisplay header{display:none}.minimalDisplay nav{display:none}.minimalDisplay aside{display:none}.minimalDisplay #pageDIV>div{min-width:99%;width:auto;left:.5%;top:1em}html.minimalDisplay{overflow-x:auto!important}html{overflow-y:scroll;font-size:14px;font-family:verdana,meiryo,sans-serif,Arial Unicode MS,Cambria Math;overflow-x:hidden;color:var(--COLOUR__TXT)}body{margin:0;background-color:var(--COLOUR__BG)}input[type=reset],input[type=submit]{font-family:verdana,meiryo,sans-serif,Arial Unicode MS,Cambria Math;font-size:1em}a img{border:none}img{max-width:100%;height:auto}header{position:absolute;z-index:990;top:-.5em;background-image:linear-gradient(var(--COLOUR__MAIN_ACCENT),var(--COLOUR__MAIN));border-bottom-right-radius:1em;border-bottom-left-radius:1em;box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)}header>:first-child>:nth-child(4){position:absolute;bottom:.67em;left:.5em}@media only screen and (max-width:16em){header>:first-child>:nth-child(4) a{display:none}header>:first-child>:nth-child(4){right:0;left:auto}}@media only screen and (max-width:11em){header>:first-child>:nth-child(4)>span>span{display:none}}#pageDIV>div{position:absolute;display:inline-block;z-index:10}table{font-size:1em}figcaption:active{opacity:1!important;-webkit-user-select:none}figcaption:hover{opacity:1!important}figcaption{transition:opacity .3s ease-out;opacity:.33}figcaption{font-style:italic;padding:1em 3em 1em 3em;border-bottom-left-radius:1em;border-bottom-right-radius:1em}header:after{box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)}figure{border:1px solid var(--COLOUR__MAIN)}figcaption{background-color:rgb(rgb(var(--COLOUR__MAIN_MILD)));color:var(--COLOUR__MAIN_OPPOSITE)}hr.smoothHR{border:0;height:1px;background-image:linear-gradient(to right,var(--COLOUR__MAIN_ACCENT),var(--COLOUR__MAIN),var(--COLOUR__MAIN_ACCENT))}hr.leftHR{border:0;height:1px;background-image:linear-gradient(to right,var(--COLOUR__MAIN),var(--COLOUR__MAIN_ACCENT))}a{color:#00f}a.blackA{color:var(--COLOUR__TXT)}a:hover{color:#c8323a!important}a.A_nomarkup{color:var(--COLOUR__TXT);text-decoration:none}nav{position:absolute;margin-left:.5%}nav ul{margin:0;padding:0;overflow:hidden}nav li{list-style:none;padding:0 0 .5em 1em}nav li:last-child{padding-bottom:0}nav a{text-decoration:none;color:var(--COLOUR__TXT);display:inline-block}figure img{max-width:97.5%;padding:1em}figure{border-radius:1em}header>:first-child{padding-top:.5em}header>:first-child>:nth-child(5) a{color:var(--COLOUR__TXT)}header>:first-child>:nth-child(4) svg{width:2.25em}header>:first-child>:nth-child(4) img,header>:first-child>:nth-child(4) svg{height:2.25em}header>:first-child>:nth-child(4)>:nth-child(6) img{margin-right:.25em}header>:first-child>:nth-child(4) span{display:inline-block;vertical-align:top;margin-top:1.25em;margin-left:.5em;font-weight:700}header>:first-child>:nth-child(4)>:nth-child(5):not(:lang(ja)){display:none}header>:first-child>:nth-child(4)>:nth-child(5) img:lang(ja){margin-right:.1em;margin-left:.0625em;width:auto}header>:first-child>:nth-child(4)>:nth-child(1){margin:0 .5em 0 0;padding:0 .5em 0 0;cursor:pointer}header>:first-child>:nth-child(4)>:nth-child(1) span{position:relative;bottom:.75em}header>:first-child>:nth-child(4)>:nth-child(7) img{width:auto}header>:first-child>:nth-child(4)>:nth-child(8) img{width:auto}@media only screen and (max-width:45em){header>:first-child>:nth-child(4)>:nth-child(6){display:none}}@media only screen and (max-width:72em){header>:first-child>:nth-child(5){display:none}#loginCheck{display:none}}li a{display:inline}footer>div>span img{width:auto;vertical-align:middle;height:3em}@media only screen and (min-width:25em){header>:first-child>:nth-child(5) a{display:inline-block!important}}@media only screen and (max-width:40em){header>:first-child>:nth-child(5){max-width:calc(100% - 24em)!important;right:.5em!important}.wwpdb_foundation_img,.wwpdb_img{display:none}}@media only screen and (max-width:40em){header>:first-child>:nth-child(5){top:5.3125em!important}header>:first-child>:nth-child(2){bottom:.75em;left:18em}header>:first-child>:nth-child(2):lang(ja){left:19em}header>:first-child>:nth-child(2):not(:lang(ja)){left:18em}}@media only screen and (max-width:16em){header>:first-child>:nth-child(4) a{display:none}header>:first-child>:nth-child(2){right:0;left:auto}}@media only screen and (max-width:27em){header{height:9em}#pageDIV>div{top:12em}header>:first-child>:nth-child(5){bottom:-.75em!important;top:initial!important}header:after{height:11em}nav{top:12em!important}}@media only screen and (max-width:11em){header>:first-child>:nth-child(4)>span>span{display:none}}@media only screen and (max-width:21em){header>:first-child>:nth-child(5){display:none}}header>:first-child>:nth-child(2){position:absolute;padding:.5em}@media only screen and (min-width:64.1315em){header>:first-child>:nth-child(2){top:.5em;right:3.5em}header>:first-child>:nth-child(2) .lb_sel{color:#c8323a}header>:first-child>:nth-child(2) .button{display:none}header>:first-child>:nth-child(2)>span{visibility:visible!important;opacity:1!important;display:block}header>:first-child>:nth-child(2) a{cursor:pointer;margin:.25em 0 0 1em;font-size:1.125em}header>:first-child>:nth-child(2) a:nth-child(1):lang(en),header>:first-child>:nth-child(2) a:nth-child(2):lang(ja),header>:first-child>:nth-child(2) a:nth-child(3):lang(zh-CN),header>:first-child>:nth-child(2) a:nth-child(4):lang(zh-TW),header>:first-child>:nth-child(2) a:nth-child(5):lang(ko){color:#c8323a}header>:first-child>:nth-child(2) br{display:none}}@media only screen and (min-width:40.0315em) and (max-width:64.15em){header>:first-child>:nth-child(2){top:.5em;right:3.5em!important}}@media only screen and (max-width:64.15em){header>:first-child>:nth-child(2)>span{border:1px solid var(--COLOUR__MAIN)}header>:first-child>:nth-child(2)>:nth-child(1){border:1px solid #ccc;border-radius:1em;padding:.33em .5em .25em 1em;box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23);cursor:pointer;font-size:.9em}header>:first-child>:nth-child(2)>:nth-child(1):lang(en):after{content:'English ▼'}header>:first-child>:nth-child(2)>:nth-child(1):lang(ja):after{content:'日本語 ▼'}header>:first-child>:nth-child(2)>:nth-child(1):lang(zh-CN):after{content:'简体中文 ▼'}header>:first-child>:nth-child(2)>:nth-child(1):lang(zh-TW):after{content:'繁體中文 ▼'}header>:first-child>:nth-child(2)>:nth-child(1):lang(ko):after{content:'한국어 ▼'}header>:first-child>:nth-child(2) a{cursor:pointer;margin:.25em 0 0 .75em;font-size:1.125em;display:block}header>:first-child>:nth-child(2)>:nth-child(2){box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23);border-radius:1em;white-space:nowrap;position:absolute;top:2.25em;left:.5em;background-color:#f8f8fc;z-index:1000;padding:.25em 1em .5em 0;opacity:0;visibility:hidden;transition:visibility .2s ease,opacity .2s ease}}header>:first-child>:nth-child(5){font-size:.8em;position:absolute;right:5em;top:9.75em;opacity:.5;padding:.25em .5em .25em 0;text-align:right;max-width:75%;max-width:calc(100% - 30em)}header>:first-child>:nth-child(5):hover{opacity:1}header>:first-child>:nth-child(5) a{margin-left:1em;display:block}footer{margin-top:1.5em;text-align:center;-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none}footer>div>:first-child a{display:inline-block;height:1.5em;padding:0 .25em 0 .25em}footer>div>:first-child a:not(:last-child){border-right:1px solid #ccc}.minimalDisplay #featuredPDBpanel,.minimalDisplay #mine_better_struct,.minimalDisplay #pdbInfoBox{display:none}#loadingImg{position:fixed;top:1em;left:1em;width:10em;height:10em;background-color:#ffffffaa;border-radius:5em;z-index:999;-webkit-backdrop-filter:blur(4px);backdrop-filter:blur(4px);visibility:hidden;opacity:0;transition:visibility .2s ease,opacity .2s ease}#loadingImg.vis{visibility:visible;opacity:1}#pdbInfoBox{position:absolute;top:-.5em;left:.5%;width:15.25%;text-align:center;height:10.5em;background-image:linear-gradient(var(--COLOUR__MAIN_ACCENT),var(--COLOUR__MAIN));border-bottom-right-radius:1em;border-bottom-left-radius:1em;box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)}#pdbInfoBox>:first-child{padding-top:1em;height:0;position:absolute}#pdbInfoBox>div>:first-child{margin:0;font-size:2.5em;font-weight:700}#pdbInfoBox>div>:nth-child(2){margin:0;font-size:.9em;padding:0 2em 0 2em;display:block}#pdbInfoBox img{width:15%;display:inline-block;margin:.5em}@media only screen and (min-width:75em){#topSearchBox{width:55%;top:4.25em}}#pdbjHeaderImg{cursor:pointer;position:absolute;padding:.2em 0 0 .5em}@media only screen and (min-width:40.001em) and (max-width:75em){#topSearchBox{width:60%;top:4em;max-width:calc(100% - 29em)}}@media only screen and (min-width:40.001em){#pdbjHeaderImg{height:6.4em}}@media only screen and (max-width:40em){#pdbjHeaderImg{height:3.65em}#topSearchBox{top:.5em;width:25%;width:calc(100% - 16em)}#featuredPDBpanel,#mine_better_struct{display:none}}@media only screen and (min-width:40.001em) and (max-width:75em){#featuredPDBpanel,#mine_better_struct{width:23.75%!important}}@media only screen and (max-width:75em){#pdbInfoBox{display:none}}#searchpaginator{border-top-left-radius:2em;border-top-right-radius:2em;z-index:920;position:fixed;bottom:0;background-color:var(--COLOUR__MAIN_ACCENT);border:1px solid #000;border-bottom:0;padding:0 .5em 0 .5em;text-align:center;overflow:hidden}#searchpaginator>:not(:last-child){border-right:1px solid #888}#searchpaginator>*{padding:.66em 1em 1em;display:inline-block;-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;text-decoration:none}#searchpaginator>p{margin:0}@media only screen and (min-width:75em){#searchpaginator{width:calc(67% - 1em - 1px);left:16.5%}}@media only screen and (max-width:75em){#searchpaginator{left:.5%;color:red}}@media only screen and (min-width:40.001em) and (max-width:75em){#searchpaginator{width:calc(74.5% - 1em - 1px)}}@media only screen and (max-width:40em){#searchpaginator{width:calc(99% - 1em - 1px);left:.5%}}#featuredPDBpanel,#mine_better_struct{position:absolute;top:-.5em;right:.5%;width:15.25%;text-align:center;height:10.5em;z-index:991;background-image:linear-gradient(var(--COLOUR__MAIN_ACCENT),var(--COLOUR__MAIN));border-bottom-right-radius:1em;border-bottom-left-radius:1em;box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)}#featuredPDBpanel>:first-child,#mine_better_struct>:first-child{height:0;position:absolute;width:100%;opacity:0;transition:opacity .33s ease;padding-top:.5em}#featuredPDBpanel>:first-child>:nth-child(1),#mine_better_struct>:first-child>:nth-child(1){display:inline;color:#00f;padding-top:0;text-align:center;color:var(--COLOUR__TXT);text-decoration:none}#featuredPDBpanel>:first-child>:nth-child(1)>div,#mine_better_struct>:first-child>:nth-child(1)>div{font-family:"Courier New";z-index:900;font-weight:700;position:relative;margin-left:auto;margin-right:auto;display:inline-block;padding:.5em;background-color:rgba(255,255,255,.67);border-bottom-left-radius:1em;border-bottom-right-radius:1em}#featuredPDBpanel>:first-child>:nth-child(1):hover>div,#mine_better_struct>:first-child>:nth-child(1):hover>div{-webkit-backdrop-filter:blur(4px);backdrop-filter:blur(4px)}#featuredPDBpanel>:first-child>:nth-child(1)>img,#mine_better_struct>:first-child>:nth-child(1)>img{margin-left:auto;margin-right:auto;margin-top:-2.125em;display:block}#featuredPDBpanel>:nth-child(2),#mine_better_struct>:nth-child(2){position:absolute;right:.5em;width:25%;bottom:1.75em;color:#00f}.linkLike{color:#00f;cursor:pointer}.linkLike:hover{color:red}.nwButton{text-align:center;border:1px solid var(--COLOUR__MAIN_BORDER);display:inline-block;border-radius:1em;font-size:1em;font-weight:700;padding:.5em 1em .5em 1em;background-color:var(--COLOUR__MAIN_MILD_SELECT);-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;box-shadow:0 3px 6px rgba(0,0,0,.16),0 3px 6px rgba(0,0,0,.23);cursor:pointer;margin-bottom:1em;font-family:inherit;font-size:1em;text-decoration:none;color:var(--COLOUR__TXT);transition:all .3s cubic-bezier(.25,.8,.25,1)}.nwButton:disabled{filter:grayscale(100%);color:grey}.nwButton:focus{outline:0}.nwButton:hover:enabled{box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)}a.nwButton:hover{box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23);color:#000!important}.grayscale{-webkit-filter:grayscale(100%);-moz-filter:grayscale(100%);-ms-filter:grayscale(100%);-o-filter:grayscale(100%);filter:grayscale(100%);filter:url("data:image/svg+xml;utf8,<svg xmlns=\'http://www.w3.org/2000/svg\'><filter id=\'grayscale\'><feColorMatrix type=\'matrix\' values=\'0.3333 0.3333 0.3333 0 0 0.3333 0.3333 0.3333 0 0 0.3333 0.3333 0.3333 0 0 0 0 0 1 0\'/></filter></svg>#grayscale");filter:gray}.unselectableText{-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none}.opacityTransition{opacity:.4s cubic-bezier(.25,.8,.25,1)}.opacityTransition2{transition:visibility .4s cubic-bezier(.25,.8,.25,1),opacity .4s cubic-bezier(.25,.8,.25,1)}.menuTransition{transition:visibility .4s cubic-bezier(.25,.8,.25,1),opacity .4s cubic-bezier(.25,.8,.25,1),height .4s cubic-bezier(.25,.8,.25,1)}.allTransition{transition:all .4s cubic-bezier(.25,.8,.25,1)}.OGhover{opacity:.25}.OGhover:hover{opacity:1}.BLOG_BOX{overflow-wrap:anywhere;padding:0 1.25em 0 3em}.BLOG_BOX pre{white-space:pre-wrap}.BLOG_BOX a{display:inline!important}.sNP{border-radius:1em;background-color:var(--COLOUR__MAIN_ACCENT);margin-bottom:1em;border:1px solid var(--COLOUR__MAIN_BORDER);box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)}.sNP>:first-child{position:relative;border-top-left-radius:16px;border-top-right-radius:16px;font-size:1em;font-weight:700;padding:.5em 1em .5em 1em;min-height:1em;background-image:linear-gradient(rgb(var(--COLOUR__MAIN_MILD)),var(--COLOUR__MAIN_ACCENT));-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;display:block;overflow-wrap:anywhere}.sNP>:nth-child(2){padding:.5em 1em 1em 1em;visibility:visible;opacity:1;height:100%;background-color:var(--COLOUR__MAIN_ACCENT);border-bottom-left-radius:1em;border-bottom-right-radius:1em}.sNP_collapse>:nth-child(2){height:0;visibility:hidden;opacity:0;margin-bottom:-1em}.sNP>h1:first-child,.sNP>h3:first-child{margin:0;font-size:1.5em;border-top-left-radius:.8em;border-top-right-radius:.8em;padding:.35em .7em .35em .7em}.sNP.ddM{box-shadow:0 3px 6px rgba(0,0,0,.16),0 3px 6px rgba(0,0,0,.23)}.sNP.ddM.sNPex>:first-child{padding:.5em 1em 1em 4em;border-radius:16px}.sNP.ddM.sNPex>:nth-child(2){z-index:999;position:absolute;background-color:var(--COLOUR__BG);color:var(--COLOUR__TXT);margin-left:.75em;border-bottom-right-radius:1em;border-bottom-left-radius:1em;border-top:none!important;overflow:hidden;height:initial;width:calc(100% - 16em);border:1px solid var(--COLOUR__MAIN_BORDER);box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)}.sNP.ddM label{cursor:pointer;-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;display:block;padding:.25em;margin:0;font-size:.9em}.sNP.ddM a{cursor:pointer;-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;display:block;padding:.25em;margin:0;font-size:.9em}.sNP.ddM label.sel{background-image:linear-gradient(to right,var(--COLOUR__MAIN_MILD_SELECT),var(--COLOUR__MAIN_ACCENT));font-weight:700;font-style:italic}.sNP.ddM label:hover{color:var(--COLOUR__MAIN_OPPOSITE)}.sNP.ddM input{display:none;color:var(--COLOUR__TXT)}.sNPex>:first-child{padding-left:3em}.sNPex>:first-child:before{position:absolute;cursor:pointer;margin-top:.33em;width:0;height:0;border-left:.75em solid transparent;border-right:.75em solid transparent;border-top:.75em solid #fff;border-bottom:0 solid transparent;transition:all .4s ease;content:'';margin-left:-2em}.sNPex>:first-child:hover:before{border-top:.75em solid var(--COLOUR__MAIN_OPPOSITE)}.sNP_collapse>:first-child:before{transform:rotate(-90deg)}.visible{opacity:1!important;visibility:visible!important}.hidden{opacity:0;visibility:hidden}.sPlane{border-radius:1em;padding:1em;background-color:var(--COLOUR__BG);margin-bottom:2em;border:1px solid var(--COLOUR__MAIN_BORDER);box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)}@media only screen and (max-width:40em){.sPlane{padding:.5em}}.fancySearch{position:relative;padding:1px 2.5em 1px 1.5em;background-color:var(--COLOUR__BG);border-radius:1em;border:1px solid #888;height:2.67em;max-height:2.67em;transition:width .4s ease,min-width .4s ease,height .4s ease,min-height .4s ease;box-shadow:0 3px 6px rgba(0,0,0,.16),0 3px 6px rgba(0,0,0,.23)}.fancySearch>:first-child{margin-top:-1px;height:2.8em;width:2.5em;padding:0 .25em 0 .25em;display:inline;position:absolute;cursor:pointer;right:0;background-color:#888;border-top-right-radius:.9em;border-bottom-right-radius:.9em;transition:all .3s cubic-bezier(.25,.8,.25,1)}.fancySearch svg>circle{stroke:white;stroke-width:7;fill:transparent}.fancySearch svg>ellipse{fill:white}.fancySearch>:first-child:hover{background-color:var(--COLOUR__MAIN_BORDER)}.fancySearch>input{vertical-align:middle;border:1px solid #888;background-color:var(--COLOUR__BG);font:1em courier new;padding:.15em .5em .15em .5em;margin:.33em 0 .125em 0;overflow:auto;height:2em;border-radius:.5em;width:95%;outline:0;color:var(--COLOUR__TXT);width:calc(100% - 2em);border:none}@media only screen and (max-width:40em){#topSearchBox.fancySearch{padding-left:.5em}}@media only screen and (max-width:27em){#topSearchBox.fancySearch{top:4.25em!important;width:calc(100% - 5em)!important}}.fancySearch>:nth-child(3){transition:top .4s ease,bottom .4s ease,left .4s ease,right .4s ease,min-width .4s ease,width .4s ease,height .4s ease,opacity .4s ease,visibility .4s ease;top:2.75em;position:absolute;width:85%;width:calc(100% - 6em);height:0;overflow:hidden;z-index:100;background-color:var(--COLOUR__BG);right:3em;margin-right:-1px;border-bottom-left-radius:1em;border-bottom-right-radius:1em;padding:.5em;border:1px solid #888;border-top-color:transparent;transition:width .4s ease,height .4s ease,opacity .4s ease,visibility .4s ease;opacity:0;visibility:hidden;box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)!important;-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none}.textBox{vertical-align:middle;border:1px solid #888;background-color:var(--COLOUR__BG);font:1em courier new;padding:.15em .5em .15em .5em;margin:.125em 0 .125em 0;overflow:auto;height:2em;border-radius:.5em;width:95%;width:calc(100% - 1.125em);outline:0;color:var(--COLOUR__TXT)}.fancySearch .closeButton{right:.25em;top:0}.closeButton{position:absolute;margin-top:.25em;right:1.1em;cursor:pointer;border-radius:1em;width:1em;height:1em;border:1px solid transparent;text-align:center;padding:.025em .275em .475em .275em;font-weight:700;text-decoration:none;color:var(--COLOUR__TXT);z-index:900;transition:top .4s ease,bottom .4s ease,left .4s ease,right .4s ease,min-width .4s ease,width .4s ease,height .4s ease,opacity .4s ease,visibility .4s ease}.closeButton:hover{border-color:var(--COLOUR__MAIN_OPPOSITE)}@media only screen and (min-width:40.001em){.tabbedPlane{left:2.5em;width:90%;width:calc(100% - 5em)}}@media only screen and (max-width:40em){.tabbedPlane{left:1em;width:95%;width:calc(100% - 2em)}}.tabbedPlane{font-weight:700;display:inline-block;position:relative;top:1px;z-index:0;margin-top:-.5em}.tabbedPlane a,.tabbedPlane span{color:var(--COLOUR__TXT);text-decoration:none;box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23);-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;transition:all .4s ease,padding 0s!important;font-size:1em;height:1.25em;padding:.5em .5em .75em .5em;display:inline-block;margin:.5em .25em 0 0;cursor:pointer;opacity:.5;position:relative;top:.25em;border:1px solid rgb(var(--COLOUR__MAIN_MILD));background-color:rgba(var(--COLOUR__MAIN_MILD),.33);border-radius:1em 1em 0 0}.tabbedPlane .tab_sel{padding-top:.75em!important;top:0!important}.tabbedPlane.bottom{z-index:10}.tabbedPlane a:hover{background-color:rgb(var(--COLOUR__MAIN_MILD));opacity:1}.tabbedPlane .tab_sel{background-image:linear-gradient(#fff,rgba(255,255,255,0));background-color:rgb(var(--COLOUR__MAIN_MILD));box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23);opacity:1}.tabbedPlane.b.tab_sel{background-image:linear-gradient(rgba(255,255,255,0),#fff)!important}.tabbedPlane .tab_sel{background-color:rgb(var(--COLOUR__MAIN_MILD))}.tabbedPlane+div{border-radius:1em;padding:1em;background-color:var(--COLOUR__BG);margin-bottom:2em;border:1px solid var(--COLOUR__MAIN_BORDER);box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23);z-index:1;position:relative}#infoBox{z-index:999;position:fixed;width:25em;bottom:.5em;right:1em;visibility:hidden;background-color:var(--COLOUR__MAIN_ACCENT);color:var(--COLOUR__TXT)}#infoBox>:nth-child(2){visibility:inherit;overflow-wrap:break-word}#infoBox>:first-child{font-size:1.5em}.optCat_p{cursor:pointer;width:1.25em;display:inline-block;font-family:courier;text-align:center}.optCat_n{cursor:pointer}.sbp_tags label{display:inline-block;margin-right:.5em}.sbp_tags input{font-size:.8em;color:var(--COLOUR__TXT)}#topSearchBox{position:absolute;right:1em;z-index:999}.pEC_tableMenu{position:absolute;border:1px solid #000;border-radius:.5em;padding:.25em;background-color:var(--COLOUR__BG);z-index:999;box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23)}.pEC_tableMenu>div{padding:.25em}.pEC_tableMenu>div.title{display:inline-block;min-height:1em}.pEC_tableMenu>div:not(.title):hover{cursor:pointer;background-color:red}.pEC_tableMenu label{padding:.25em;display:block;cursor:pointer}.pEC_tableMenu label:hover{background-color:#eee}.pEC_iconButton{border:1px solid #000;border-radius:.8em;width:1.6em;display:inline-block;text-align:center;font-weight:700;line-height:1.6em;margin-left:.33em;font-size:.75em;vertical-align:top;padding:0!important;position:absolute;right:0;top:-.33em}.pEC_iconButton:hover{color:red;border-color:red;cursor:pointer}.entryMenu{border-bottom:1px dotted;cursor:pointer}.entryMenu:after{content:'\25be';border-radius:1em;padding-left:.175em;padding-right:.175em}.entryMenu:hover:after{background-color:#ddd}#pdb_img_popup{border-radius:.5em;width:15%;border:1px solid var(--COLOUR__MAIN);position:absolute;z-index:999;box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23);transition:visibility .2s ease,opacity .2s ease;visibility:hidden;opacity:0;padding:.25em}#pdb_img_popup>img{width:100%}#pdb_img_popup>div{position:absolute}.molmil_container{width:100%;position:relative}.aspect_1to1{padding-top:100%}.aspect_2to1{padding-top:50%}.molmil_container>iframe{position:absolute;top:0;height:100%;width:100%;border:none}.codeQuoteBox{border:1px solid #000;margin-left:1em;margin-right:1em;font-family:courier;background-color:var(--COLOUR__MAIN_MILD_SELECT);border:solid thin #99a;padding:.5em;overflow:auto}.dragPlane{position:absolute;z-index:999}.dragPlane .closeButton{margin-top:-1.33em}.dragPlane>:first-child{cursor:move}.newweb-auto-date:not(.not){cursor:default;text-decoration-style:dashed;text-decoration-line:underline}</style><style data-module="main">.servicebrowser_tt .fancySearch{margin-bottom:1em}.servicebrowser_tt button{width:100%}@media only screen and (max-width:60em){.servicebrowser_tt>tbody>tr>td{display:block}.servicebrowser_tt>tbody>tr>td:nth-child(2){width:auto!important}}.servicebrowser_tt{width:100%;overflow-wrap:anywhere}.servicebrowser_tt>tbody>tr>td:nth-child(2){width:25em}#sB_resultsBox table>tbody>tr>td:first-child{width:25em}#sB_fancySearch{box-shadow:0 3px 6px rgba(0,0,0,.16),0 3px 6px rgba(0,0,0,.23)}#sB_resultsBox table{border-collapse:collapse}#sB_resultsBox table>tbody>tr:nth-child(odd){background-color:var(--COLOUR__SWITCH_1)}#sB_resultsBox table>tbody>tr:nth-child(2n){background-color:var(--COLOUR__SWITCH_3)}#sB_resultsBox table>tbody>tr>td:first-child{width:25%}#sB_resultsBox table>tbody>tr>td:nth-child(2){width:75%}.bPlane{border:1px solid var(--COLOUR__MAIN_BORDER);border-radius:1em;font-size:1em;font-weight:700;background-image:linear-gradient(rgb(var(--COLOUR__MAIN_MILD)),#fff);-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;box-shadow:0 10px 20px rgba(0,0,0,.19),0 6px 6px rgba(0,0,0,.23);margin-bottom:1em;display:block;overflow:hidden}.bPlane._small{padding:1em}.bPlane._small>img{display:block;margin:auto}.minH1{font-size:1em;display:inline;font-weight:400}.bPlane>img[alt=COVID-19]{display:block;margin:auto;image-rendering:-webkit-optimize-contrast;image-rendering:optimizequality}.bPlane._small>img[alt=EMnavi]{background-color:#585;margin:-1em;padding:1em;-webkit-mask-image:radial-gradient(rgba(0,0,0,1),33%,rgba(0,0,0,1),70%,rgba(0,0,0,0),95%,rgba(0,0,0,0));mask-image:radial-gradient(rgba(0,0,0,1),33%,rgba(0,0,0,1),70%,rgba(0,0,0,0),95%,rgba(0,0,0,0))}.bPlane._small:nth-child(2){padding:.5em}.bPlane._small:nth-child(4){padding:0}.bPlane:nth-child(3) :nth-child(2){position:relative;bottom:2.5em;left:.8em;font-size:50%;height:0;max-width:43%;text-align:right;bottom:2.5em}@media only screen and (min-width:640px) and (max-width:869px){.bPlane:nth-child(3) :nth-child(2){bottom:4em}}#home>#news>:first-child a{margin-left:.7em}#home>#news>:first-child img{height:1em;vertical-align:middle;margin-top:-.35em;width:auto}#home>#news>:nth-child(2){margin-left:1.25em;padding-right:2.25em}#home>#news>:nth-child(2) td:first-child{vertical-align:top;width:8em;padding:.5em .5em .5em 1em}#home>#news>:nth-child(2) table{border-collapse:collapse;width:100%}#home>#news>:nth-child(2) tr:nth-child(2n){background-color:var(--COLOUR__SWITCH_1)}#home>#news>:nth-child(2) tr:nth-child(odd){background-color:var(--COLOUR__SWITCH_3)}#version_table tr>td:first-child{font-weight:700}</style><link rel="canonical" href="https://pdbj.org/help/giraf" /><link rel="alternate" href="https://pdbj.org/help/giraf" hreflang="x-default" /><link rel="alternate" href="https://pdbj.org/help/giraf?lang=ja" hreflang="ja" /><link rel="alternate" href="https://pdbj.org/help/giraf?lang=zh-CN" hreflang="zh-CN" /><link rel="alternate" href="https://pdbj.org/help/giraf?lang=zh-TW" hreflang="zh-TW" /><link rel="alternate" href="https://pdbj.org/help/giraf?lang=ko" hreflang="ko" /> <meta charset="utf-8"><meta name="description" content="PDBj maintains the single global PDB/BMRB/EMDB archives of macromolecular structures and provides integrated tools for searching & analyzing PDB data"><meta name="thumbnail" content="/newweb/media/pdbj_logo.svg"><title>GIRAF - Protein Data Bank Japan</title></head> <body> <img alt="Loading" src="/newweb/media/loading.png" id="loadingImg" class="vis"><div id="pageDIV"><header><div><a href="/"><img id="pdbjHeaderImg" src="/newweb/media/pdbj_logo.svg" alt="PDBj"></a><div class="unselectableText"><span onclick="newweb.call('core.lang_btn_click',this,event)"></span><span><a title="English" onclick="newweb.call('core.lang_click',this,event)" data-lang="en">English</a><a title="日本語" onclick="newweb.call('core.lang_click',this,event)" data-lang="ja">日本語</a><a title="简体中文" onclick="newweb.call('core.lang_click',this,event)" data-lang="zh-CN">简体中文</a><a title="繁體中文" onclick="newweb.call('core.lang_click',this,event)" data-lang="zh-TW">繁體中文</a><a title="한국어" onclick="newweb.call('core.lang_click',this,event)" data-lang="ko">한국어</a></span></div><div class="fancySearch" id="topSearchBox"><span title="Search" onclick="newweb.call('core.omniSearchClick',this,event)"><svg xmlns="http://www.w3.org/2000/svg" width="100%" height="100%" viewBox="0 0 100 100"><circle cx="33" cy="33" r="22"></circle><ellipse cx="67" cy="67" rx="8" ry="25" transform="rotate(-45, 67, 67)"></ellipse></svg></span><input type="text" title="Search pdbj.org" placeholder="Search pdbj.org" data-name="EVERYTHING" onfocus="newweb.call('core.oS_focus',this,event)" onblur="newweb.call('core.oS_blur',this,event)" onkeydown="newweb.call('core.oS_keydown',this,event)" onkeyup="newweb.call('core.oS_keyup',this,event)"><div><div class="closeButton" title="Close" onclick="newweb.call('core.oS_close',this,event)">✖</div><div></div></div></div><div class="unselectableText"><span onclick="newweb.call('core.toggleMenu',this,event)"><svg xmlns="http://www.w3.org/2000/svg"><path d="M4,10h24c1.104,0,2-0.896,2-2s-0.896-2-2-2H4C2.896,6,2,6.896,2,8S2.896,10,4,10z M28,14H4c-1.104,0-2,0.896-2,2 s0.896,2,2,2h24c1.104,0,2-0.896,2-2S29.104,14,28,14z M28,22H4c-1.104,0-2,0.896-2,2s0.896,2,2,2h24c1.104,0,2-0.896,2-2 S29.104,22,28,22z" fill="red"></path></svg><span> Menu</span></span><a href="https://www.facebook.com/PDBjapan" target="_blank" rel="noopener"><img src="/newweb/media/icons/fbicon_32.png" title="PDBj@Facebook" alt="PDBj@Facebook" width="32" height="32"></a><a href="https://x.com/PDBj_en" target="_blank" rel="noopener"><img src="/newweb/media/icons/xicon_32.png" title="PDBj@X(formerly Twitter)" alt="PDBj@X(formerly Twitter)" width="32" height="32"></a><a href="https://bsky.app/profile/pdbjen.bsky.social" target="_blank" rel="noopener"><img src="/newweb/media/icons/bsicon_32.png" title="PDBj@BlueSky" alt="PDBj@BlueSky" width="32" height="32"></a><a href="https://www.youtube.com/user/PDBjmovie" target="_blank" rel="noopener"><img src="/newweb/media/icons/yt_icon.png" title="PDBj@YouTube" alt="PDBj@YouTube" width="64" height="64"></a><a href="https://foundation.wwpdb.org/" target="_blank" rel="noopener" class="wwpdb_foundation_img"><img src="/newweb/media/wwpdb_foundation.png" title="wwPDB Foundation" alt="wwPDB Foundation" width="109" height="32"></a><a href="https://wwpdb.org/" target="_blank" rel="noopener" class="wwpdb_img"><img src="/newweb/media/wwpdb_logo.png" title="wwPDB" alt="wwPDB" width="187" height="58"></a><a href="https://pdbj.org/info/donation" target="_blank" rel="noopener"><img src="/newweb/media/wani.png" title="Donate" alt="Donate" width="187" height="58"></a></div><div><a title="RCSB Protein Data Bank" href="https://www.rcsb.org/" target="_blank" rel="noopener">RCSB PDB</a><a title="Protein Data Bank in Europe" href="https://www.ebi.ac.uk/pdbe/" target="_blank" rel="noopener">PDBe</a><a title="Biological Magnetic Resonance Data Bank" href="https://bmrb.io/" target="_blank" rel="noopener">BMRB</a><a title="PDBj Advanced search" href="/rdb/build">Adv. Search</a><a title="PDBj Omni Search Help" href="/help/omni-search">Search help</a></div></div></header><div><main id=""><div class="sNP" typeof="Article"><h1 property="name headline">GIRAF</h1><div><div class="OGhover opacityTransition2 _langList_" style="margin-left: 3em;"><span>This page is also available in: </span><a title="日本語" href="/help/giraf?lang=ja" style="margin-right: 0.75em;">日本語</a><hr class="leftHR"></div><div property="articleBody" class="BLOG_BOX"> <p><strong>The GIRAF service terminated on 30th April 2019. Thank you for using so long.</strong></p> <h2 id="H-mo22w2aj">[The URL]</h2> <p><a href="/giraf/">https://pdbj.org//giraf/</a></p> <h2 id="H-om4m2fx0i3ux">[Introduction to GIRAF]</h2> <p>GIRAF is a similarity search service for ligand binding sites available at <a href="/giraf/">https://pdbj.org//giraf/</a>. For a given PDB ID or uploaded PDB file, <a href="/help/giraf">GIRAF</a> searches for known ligand binding sites in the PDB that are similar to substructures of the query.</p> <h2 id="H-t4fgslqmqk1h">[How to execute a GIRAF search]</h2> <h3 id="H-t4fgsmjwmpan">Input</h3> <p>There are two ways to provide your query structure, by either</p> <ol> <li>specifying a PDB ID, or</li> <li>uploading a PDB-formatted file.</li> </ol> <h3 id="H-3iieposrlw2ey">Limiting search to specific protein subunits (optional)</h3> <p>Optionally, you can specify chain IDs so that the search is performed only for the specified chains. The default isallwhich means all the protein chains (longer than 25 amino acid residues) are treated. The chain IDs must be those that appear in PDB-format files (i.e., auth_asym_id of mmCIF or PDBML). When specifying multiple chain IDs, they must be separated by comma (no space).</p> <h3 id="H-28sa1wlixkcfr">Email notification (optional)</h3> <p>You can input an email address to which a notification of the GIRAF search result will be sent.</p> <h3 id="H-efvwgqnnfcua">Executing a search</h3> <p>After specifying a query and clicking the <strong>submit</strong> button, you will find the result page, which will contain no results yet. Usually, search results will be available in 10-30 minutes, but large query proteins may take longer. If you have specified your email address, an email will be sent when the search is completed. Otherwise, you should bookmark the result page so that you can refer to it later.</p> <h2 id="H-24ccdhss6wf43">[How to examine the GIRAF results]</h2> <p>When a GIRAF search is completed, the result page will show a table of significant hits. The result page will be deleted after one week.</p> <p>The table contains the following columns:</p> <dl> <dt>rank</dt> <dd> <p>The rank of a hit in terms of the normalized GIRAF score ( <em>score</em> ).</p> </dd> <dt>PDB</dt> <dd> <p>The PDB ID of the hit.</p> </dd> <dt>align</dt> <dd> <p>The link to an alignment page with structure superposition.</p> </dd> <dt>motif</dt> <dd> <p>The link to the summary page of the corresponding structural motif. The structural motifs are those described in Kinjo and Nakamura (to appear in <em>Structure</em> ).</p> </dd> <dt>ligand</dt> <dd> <p>PDB chemical component ID except for polymeric molecules such as polypeptide (less than 25 amino acid residues), DNA (polydeoxyribonucleotide), RNA (polyribonucleotide), or sugar. They are linked to the <a href="http://www.ebi.ac.uk/pdbe/" rel="nofollow noopener" target="_blank">PDBe</a> (formerly MSD) <a href="http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl" rel="nofollow noopener" target="_blank">MSDChem</a> database (except for polymeric molecules).</p> </dd> <dt>protein</dt> <dd> <p>Description of the PDB entry.</p> </dd> <dt>score</dt> <dd> <p>Normalized GIRAF score. This is a raw GIRAF score multiplied by the squared <em>inverse document frequency (IDF)</em> of the template binding site.</p> </dd> <dt>P-value</dt> <dd> <p>The probability of finding the hit by chance.</p> </dd> <dt>RMSD</dt> <dd> <p>The root-mean-square deviation of the aligned atoms.</p> </dd> <dt>Nali</dt> <dd> <p>The number of aligned atom pairs.</p> </dd> </dl> <h3 id="H-1xbaprv0j9cm">Sorting the results</h3> <p>You may sort the results according to score, P-value, PDB ID, ligand (chemical component ID), RMSD, and Nali by selecting these keys from the menu bar and clicking the <em>submit</em> button.</p> <h3 id="H-3i7sfcajhqmab">Examining all the hits</h3> <p>By default, the result page only shows the representative ligand binding sites. If you want to look at all the hits, you may check the <em>all hits</em> button and click the <em>submit</em> button.</p> <p>The result page is an XML file containing the list of matching ligand binding sites. Thus, if you are familiar with XML processing, you can save the results into a file, parse it with your own program, and use them for your further study. Alternatively, you can convert the result page into an HTML format which can be saved on you computer.</p> <h2 id="H-2akzjufxifffy">[Using the alignment page]</h2> <p>By following the <em>show</em> link in the <em>align</em> column of the result page, you may visually examine the ligand binding sites and the ligand superposed onto the query structure, using a <a href="/help/jv">jV</a> applet. The atom-atom correspondence between the query and the template ligand binding site (i.e., the structural alignment) is also shown as a table.</p> <h3 id="H-1c3yvvozbhrvs">Alignment page as PDBML-extatom file.</h3> <p>The alignment page is a superset of the PDBML-extatom format. Therefore, you can save the alignment page as an XML file on your computer, and use <a href="/help/jv">jV</a> for closer examination of the superposition. Note, however, that the alignment page contains only the transformed ligand binding site so that you should load your query structure separately in addition to the alignment page to see the actual superposition.</p> <h2 id="H-334umlo15gj">[References]</h2> <ol> <li><a href="http://dx.doi.org/10.2142/biophysics.3.75" rel="nofollow noopener" target="_blank">Similarity search for local protein structures at atomic resolution by exploiting a database management system.</a><br> Kinjo, A.R.; Nakamura, H. <em>BIOPHYSICS</em> <strong>3</strong> :75-84 (2007).</li> <li><a href="http://dx.doi.org/10.1016/j.str.2008.11.009" rel="nofollow noopener" target="_blank">Comprehensive structural classification of ligand binding motifs in proteins.</a><br> Kinjo, A.R.; Nakamura, H. <em>Structure</em> <strong>17</strong> :234-246 (2009)</li> </ol></div><div style="margin-left: 3em; padding-bottom: 1.25em;"><hr class="leftHR"><div style="font-size: 0.75em;"><span property="datePublished">Created: 2019-05-09</span> <span style="color: #BFBFBF;">(last edited: more than 1 year ago)</span><span style="display: none;" property="dateModified">2019-05-09</span></div></div></div></div></main><aside id=""></aside><footer><div class="sPlane"><div><a title="Help" href="/help">Help</a><a title="Contact us" href="/contact">Contact us</a><a title="Terms and Conditions" href="/info/terms-conditions">Terms and Conditions</a><a title="Privacy policy" href="/info/privacy-policy">Privacy policy</a></div><hr><div></div><span><img alt="PDBj" width="300" height="114" src="/newweb/media/default.svg"> is supported by <img alt="JST" width="102" height="88" src="/newweb/media/jst_logo.svg"><img alt="NBDC" width="345" height="114" src="/newweb/media/nbdc_logo.svg"> and is a member of <a href="https://jbioinfo.jp/" target="blank" rel="nofollow noopener"><img alt="JBI" width="219" height="61" src="/newweb/media/jbi.png"></a></span><hr><div>Copyright © 2013-2025 Protein Data Bank Japan</div></div></footer></div><nav id="sideMenu"><div class="sNP sNPex" id="sideMenu_HOME"><div onclick="newweb.call('core.explane_click',this,event)">Home</div><ul><li data-desc="PDBj top page" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Top Page" href="/">Top Page</a></li><li data-desc="Statistics for PDB content distribution and growth" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Statistics" href="/info/statistics">Statistics</a></li><li data-desc="Help documents for each PDBj service" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Help" href="/help">Help</a></li><li data-desc="Frequently asked questions" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="FAQ" href="/help/faq">FAQ</a></li><li data-desc="Contact Protein Data Bank Japan" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Contact Us" href="/contact">Contact Us</a></li><li data-desc="Cite PDBj, our services or PDB entries and Terms and Conditions" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Cite Us / Terms and Conditions" href="/info/cite-us">Cite Us / Terms and Conditions</a></li><li data-desc="Links to related organizations" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Links" href="/info/links">Links</a></li><li data-desc="PDBj settings" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Settings" href="/settings">Settings</a></li></ul></div><div class="sNP sNPex" id="sideMenu_DATA_DEPOSITION"><div onclick="newweb.call('core.explane_click',this,event)">Data deposition (OneDep)</div><ul><li data-desc="About data deposition" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Help" href="/info/data-deposition">Help</a></li><li data-desc="Deposit structures determined by X-ray diffraction, Electron Microscopy or NMR method" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Deposition to PDB, EMDB or BMRB" href="https://deposit-pdbj.wwpdb.org/deposition" target="_blank" rel="noopener">Deposition to PDB, EMDB or BMRB</a></li></ul></div><div class="sNP sNPex" id="sideMenu_DATA_DOWNLOAD"><div onclick="newweb.call('core.explane_click',this,event)">Download</div><ul><li data-desc="Download PDB data using FTP or rsync protocol" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Download PDB archive / snapshot archive" href="/info/archive">Download PDB archive / snapshot archive</a></li></ul></div><div class="sNP sNPex" id="sideMenu_NEW_FORMAT"><div onclick="newweb.call('core.explane_click',this,event)">Standard format</div><ul><li data-desc="Browse PDBx/mmCIF Resources" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="PDBx/mmCIF Resources" href="/info/new-format">PDBx/mmCIF Resources</a></li><li data-desc="Convert the PDB format and PDBx/mmCIF files to the other format." onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Format Conversion" href="https://mmcif.pdbj.org/converter/index.php?l=en" target="_blank" rel="noopener">Format Conversion</a></li><li data-desc="Modify, merge and validate PDBx/mmCIF and other STAR-formatted files" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="PDBx/mmCIF editor" href="/cif-editor/" target="_blank" rel="noopener">PDBx/mmCIF editor</a></li></ul></div><div class="sNP sNPex" id="sideMenu_QUICK_LINKS"><div onclick="newweb.call('core.explane_click',this,event)">Quick links</div><ul><li><a title="Help" href="/help/quick-links-menu" target="mD_*">Help</a></li><li data-desc="Show list of non-PDB format compatible entries" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="non-PDB format compatible" href="/list/pdb-legacy-incompatible">non-PDB format compatible</a></li><li data-desc="Show list of Group Depositions entries" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Group Depositions" href="/list/pdb-group-depositions">Group Depositions</a></li><li data-desc="Show list of chemical component entries (chem_comp)" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Chemical Component entries" href="/search/chemie?query=*">Chemical Component entries</a></li><li data-desc="Show latest released or updated entries" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Latest entries" href="/pdbj-update">Latest entries</a></li></ul></div><div class="sNP sNPex" id="sideMenu_SEARCH"><div onclick="newweb.call('core.explane_click',this,event)">Search services</div><ul><li><a title="Help" href="/help/search-menu" target="mD_*">Help</a></li><li data-desc="Search using PDBj Mine (old advanced search)" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Search PDB (PDBj Mine)" href="/search/pdb-filter">Search PDB (PDBj Mine)</a></li><li data-desc="Search using PDBj Mine (advanced search)" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Search PDBj RDB" href="/rdb/build">Search PDBj RDB</a></li><li data-desc="Search chemical entries (chem_comp)" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Chemie search" href="/search/chemie-filter">Chemie search</a></li><li data-desc="Search entries in the biomolecule NMR database BMRB" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Search BMRB" href="https://bmrbj.pdbj.org/index_en.html" target="_blank" rel="noopener">Search BMRB</a></li><li data-desc="Search molecules with similar sequences" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Sequence-Navigator" href="/seqnavi">Sequence-Navigator</a></li><li data-desc="Search molecules with similar structures (replaces Structure Navigator)" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="DASH" href="/info/dash">DASH</a></li><li data-desc="Browse 3D electron microscopy (3D-EM) data of biological molecules and assemblies" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="EM Navigator" href="/emnavi/" target="_blank" rel="noopener">EM Navigator</a></li><li data-desc="Shape similarity search of macromolecules" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Omokage search" href="/emnavi/omo-search.php?lang=en" target="_blank" rel="noopener">Omokage search</a></li><li data-desc="Sequence-Derived Structural Alignment Weights --- Search functional annotations that identifies conserved sequence and structural motifs in query proteins" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="SeSAW" href="/info/sesaw">SeSAW</a></li><li data-desc="Search PDB data in RDF format" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="wwPDB/RDF" href="https://rdf.wwpdb.org/" target="_blank" rel="noopener">wwPDB/RDF</a></li><li data-desc="SPARQL endpoints for comprehensive RDF graphs" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="RDF Portal" href="https://rdfportal.org" target="_blank" rel="noopener">RDF Portal</a></li><li data-desc="Search status of unreleased PDB entries" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Status search" href="/search/status-filter">Status search</a></li></ul></div><div class="sNP sNPex" id="sideMenu_MOLECULAR_VIEWERS"><div onclick="newweb.call('core.explane_click',this,event)">Molecular Viewers</div><ul><li><a title="Help" href="/help/molecular-viewers" target="mD_*">Help</a></li><li data-desc="About jV, an interactive 3D viewer program to visualize structure of protein and nucleic acid molecules" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="jV: Graphic Viewer" href="/jv/index.html" target="_blank" rel="noopener">jV: Graphic Viewer</a></li><li data-desc="Molmil, a new molecular viewer developed for a web environment with the intent to be usable on as many platforms as possible" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Molmil: WebGL Mol. Viewer" href="/help/molmil">Molmil: WebGL Mol. Viewer</a></li></ul></div><div class="sNP sNPex" id="sideMenu_GSS"><div onclick="newweb.call('core.explane_click',this,event)">Services & Softwares</div><ul><li><a title="Help" href="/help/service-software-menu" target="mD_*">Help</a></li><li data-desc="Watch, move and enjoy 3D structures of biological molecules" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Yorodumi" href="/emnavi/quick.php?" target="_blank" rel="noopener">Yorodumi</a></li><li data-desc="Perform three-dimensional structure alignment" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="ASH" href="/info/ash">ASH</a></li><li data-desc="Calculates multple sequence alignments from sequences and structures" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="MAFFTash" href="/info/mafftash">MAFFTash</a></li><li data-desc="Download NMR related Tools" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="NMRToolBox" href="https://bmrbj.pdbj.org/en/nmr_tool_box.html" target="_blank" rel="noopener">NMRToolBox</a></li><li data-desc="A superimposition program of atomic models and 3D density maps" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="gmfit" href="/gmfit/" target="_blank" rel="noopener">gmfit</a></li><li data-desc="Predicts one-dimensional protein structures from amino acid sequence" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="CRNPRED" href="/crnpred/" target="_blank" rel="noopener">CRNPRED</a></li><li data-desc="A structural homology modeling program which threads a specific amino-acid sequence onto a specific PDB structure" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Spanner" href="/info/spanner">Spanner</a></li><li data-desc="Sequence to Function Annotation Server, for predicting the structure of an amino acid sequence" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="SFAS" href="/info/sfas">SFAS</a></li><li data-desc="Finding and modeling of 3D structures of complexes" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="HOMCOS" href="https://homcos.pdbj.org/?LANG=en" target="_blank" rel="noopener">HOMCOS</a></li></ul></div><div class="sNP sNPex" id="sideMenu_DDB"><div onclick="newweb.call('core.explane_click',this,event)">Derived databases</div><ul><li><a title="Help" href="/help/derived-databases-menu" target="mD_*">Help</a></li><li data-desc="Electrostatic-surface of Functional site, a database for molecular surfaces of proteins' functional sites" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="eF-site" href="/eF-site/" target="_blank" rel="noopener">eF-site</a></li><li data-desc="A web server to search for the similar ligand binding sites for the uploaded coordinate file" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="eF-seek" href="/eF-seek/top.do" target="_blank" rel="noopener">eF-seek</a></li><li data-desc="A web service to calculate the molecular surface of the up-loaded file" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="eF-surf" href="/eF-surf/top.do" target="_blank" rel="noopener">eF-surf</a></li><li data-desc="A database of NMA of PDB data using elastic network model in torsional angle space" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="ProMode Elastic" href="/promode-elastic">ProMode Elastic</a></li></ul></div><div class="sNP sNPex" id="sideMenu_ES"><div onclick="newweb.call('core.explane_click',this,event)">Educational service</div><ul><li><a title="Help" href="/help/educational-services-menu" target="mD_*">Help</a></li><li data-desc="Encyclopedia of Protein Structures, a dictionary with pictures of the protein three-dimensional structures" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="eProtS" href="/info/eprots">eProtS</a></li><li data-desc="Introduction to biological macromolecules written by Dr. David S. Goodsell of RCSB" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Molecule of the Month" href="https://pdb101.rcsb.org/motm/" target="_blank" rel="noopener">Molecule of the Month</a></li><li data-desc="Material of previous workshops such as handouts and movies" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Previous workshop" href="/info/previous-workshop">Previous workshop</a></li><li data-desc="The snake game of amino acid and the pelmanism of amino acid/protein" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Games" href="/games">Games</a></li><li data-desc="Make molecule models with paper" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Papermodels" href="https://numon.pdbj.org/papermodel/?l=en" target="_blank" rel="noopener">Papermodels</a></li></ul></div><div class="sNP sNPex" id="sideMenu_ABOUT"><div onclick="newweb.call('core.explane_click',this,event)">About PDBj</div><ul><li><a title="Help" href="/help/customizations" target="mD_*">Help</a></li><li data-desc="The list of papers and books involved in PDBj" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Publications" href="/info/publications">Publications</a></li><li data-desc="The newsletters and public relations resources published by PDBj" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Newsletters / Public Relations Resources" href="/info/publicresources">Newsletters / Public Relations Resources</a></li><li data-desc="The list of the PDBj members" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="PDBj Members" href="/info/staff">PDBj Members</a></li><li data-desc="The list of the PDBj Advisory Committee" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="PDBj Advisory Committee" href="/info/pdbjac">PDBj Advisory Committee</a></li><li data-desc="About the privacy policy" onmouseover="newweb.call('core.menu_mouseover',this,event)" onmouseout="newweb.call('core.menu_mouseout',this,event)"><a title="Privacy Policy" href="/info/privacy-policy">Privacy Policy</a></li></ul></div></nav><span id="pdbInfoBox"><div><p>234136</p><p>PDB entries from 2025-04-02</p><a href="/info/statistics"><img alt="PDB statistics" width="72" height="72" src="/newweb/media/statistics.png"></a><a href="/pdbj-update"><img alt="PDBj update info" width="72" height="72" src="/newweb/media/pdbj-update.png"></a><a href="/contact"><img alt="Contact PDBj" width="72" height="72" src="/newweb/media/contact.png"></a><a href="//numon.pdbj.org" target="_blank" rel="nofollow noopener"><img alt="numon" width="72" height="72" src="/newweb/media/numon_en.png"></a></div></span></div><div class="sNP opacityTransition" id="infoBox"><div></div><div></div></div><script fetchpriority="low" type="module" src="./newweb/js/core.js"></script><script fetchpriority="low" type="module" src="./newweb/js/main.js"></script><script nomodule src="./newweb/js/legacy.js"></script></body></html>