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hidden" id="602c57cf3fed9e549afd7921"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/search-and-browse/browse-options/mesh">MeSH</a></td></tr></table></div><div class="item hidden" id="6080adaaec901916050494bc"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/search-and-browse/browse-options/membrane-protein-opm">Membrane Protein (OPM)</a></td></tr></table></div><div class="item hidden" id="602c57ae3fed9e549afd7920"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/search-and-browse/browse-options/molecular-function">Molecular Function</a></td></tr></table></div><div class="item hidden" id="602c5a1e3fed9e549afd7925"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/search-and-browse/browse-options/membrane-protein-mpstruc">Membrane Protein (mpstruc)</a></td></tr></table></div><div class="item hidden" id="602c57133fed9e549afd791d"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/search-and-browse/browse-options/protein-symmetry">Protein Symmetry</a></td></tr></table></div><div class="item hidden" id="602c57603fed9e549afd791e"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/search-and-browse/browse-options/scop-e">SCOP-e</a></td></tr></table></div><div class="item hidden" id="6141014def055f03d1f222d4"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/search-and-browse/browse-options/scop2">SCOP2</a></td></tr></table></div><div class="item hidden" id="602c56f13fed9e549afd791c"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/search-and-browse/browse-options/source-organism">Source Organism</a></td></tr></table></div><div class="group show" id="618271c92a7d828464a7d146" onclick="toggle(&quot;618271c92a7d828464a7d146&quot;)"><table><tr><td style="padding-left: 4px">Exploring a 3D Structure</td><td><span class="glyphicon glyphicon-triangle-bottom" 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24px"><a href="/docs/exploring-a-3d-structure/experiment">Experiment</a></td></tr></table></div><div class="item hidden" id="618272fb04fb9835c6ae1896"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/sequence">Sequence</a></td></tr></table></div><div class="item hidden" id="6182730904fb9835c6ae1897"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/genome">Genome</a></td></tr></table></div><div class="item hidden" id="6182731a04fb9835c6ae1898"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/ligands">Ligands</a></td></tr></table></div><div class="item hidden" id="6182732a04fb9835c6ae1899"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/versions">Versions</a></td></tr></table></div><div class="group show" id="5fd3e3a6eb210c2c5632d098" 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id="5ee253237f50f44e6aa4fb22"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/3d-viewers/mol*/mol*-cheat-sheet">Mol* Cheat Sheet</a></td></tr></table></div><div class="item hidden" id="60075352c5ab5836659ab2e3"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/3d-viewers/jmol">Jmol</a></td></tr></table></div><div class="item hidden" id="65a4b499c76ca3abcc925d0d"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/3d-viewers/ngl-to-mol*-ui-migration-guide">NGL to Mol* UI Migration Guide</a></td></tr></table></div><div class="group show" id="6256b2b3b4396e45e97bf3de" onclick="toggle(&quot;6256b2b3b4396e45e97bf3de&quot;)"><table><tr><td style="padding-left: 4px">Grouping Structures</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph6256b2b3b4396e45e97bf3de"></span></td></tr></table></div><div class="item hidden" id="62fbafaf3b6e49562fa5c055"><table><tr><td class="title" style="padding-left: 24px"><a 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href="/docs/sequence-viewers/protein-sequence-alignment-view">Protein Sequence Alignment View</a></td></tr></table></div><div class="item show" id="5fc7f2843fb4b83beb6a7a3d"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/sequence-viewers/genome-view">Genome View</a></td></tr></table></div><div class="group show" id="60132e62aeeea33d3f095fa8" onclick="toggle(&quot;60132e62aeeea33d3f095fa8&quot;)"><table><tr><td style="padding-left: 4px">Tools</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph60132e62aeeea33d3f095fa8"></span></td></tr></table></div><div class="item hidden" id="60132e6a610d04019e01d4c2"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/tools/pairwise-structure-alignment">Pairwise Structure Alignment</a></td></tr></table></div><div class="group show" id="600217ee5b6ad53203751b79" onclick="toggle(&quot;600217ee5b6ad53203751b79&quot;)"><table><tr><td style="padding-left: 4px">Programmatic Access</td><td><span 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href="/docs/additional-resources/structure-validation-and-quality">Structure Validation and Quality</a></td></tr></table></div></div></div></div><div class="col-lg-9 col-md-8 col-sm-12 content-item"><div data-elastic-include><h5 class="menu-path">Sequence Viewers</h5><h1>Sequence Annotations Viewer</h1><div><div style="padding-left:40px;">○ <a href="#responsive-and-interactive-properties">Responsive and Interactive Properties</a></div> <div style="padding-left:40px;">○ <a href="#conventions">Conventions</a></div> <div style="padding-left:40px;">○ <a href="#structure-summary-page--sequence-tab">Structure Summary Page - Sequence Tab</a></div> <div style="padding-left:40px;">○ <a href="#structure-summary-page--main-tab">Structure Summary Page - Main Tab</a></div> <div style="padding-left:40px;">○ <a href="#feature-tooltips">Feature Tooltips</a></div> <div style="padding-left:40px;">○ <a href="#for-developers">For Developers</a></div> <p>The Sequence Annotations Viewer provides graphical summaries of PDB protein biological and structural features and their relationships with <a href="https://www.uniprot.org" target="_blank" rel="noopener">UniProtKB</a> entries. Protein alignments and features are loaded from RCSB PDB web services including the main data <a href="https://data.rcsb.org/" target="_blank" rel="noopener">API</a> and the <a href="https://1d-coordinates.rcsb.org/" target="_blank" rel="noopener">1D Coordinate Server</a>. These resources integrate information from multiple resources and databases. Structural features such as secondary structure, angle/distance outliers, protein-ligand binding sites or disulfide bridges, are extracted from the PDB structural data. Additionally, structural domains are annotated from <a href="https://www.cathdb.info/" target="_blank" rel="noopener">CATH</a> and <a href="https://scop.berkeley.edu" target="_blank" rel="noopener">SCOPe</a> databases. Biochemical and biomedical features are collected from the <a href="https://www.uniprot.org" target="_blank" rel="noopener">UniProtKB</a> database and mapped onto PDB sequences.</p> <a class="content-anchor" id="responsive-and-interactive-properties"></a> <h3>Responsive and Interactive Properties</h3> <ul style="list-style-type:disc;"> <li> Zoom using the mouse scroll (wheel) or the mousepad/touchpad to see more details and to show the sequence of amino acids </li> <li> To zoom using the mousepad/touchpad hover over the Sequence Annotations Viewer, and move/drag 2 fingers in an up and down motion </li> <li> Once zoomed, left click and drag to move the panel left or right (using either a mouse or touchpad) </li> <li> Left click on a feature to highlight the annotated region or right click to select and highlight a custom area </li> <li>Hovering over track features will display a legend at the top right corner of the viewer (see <a href="#feature-tooltips">Feature Tooltips</a>)</li> </ul> <div style="height: 20px;"></div><a class="content-anchor" id="conventions"></a> <h3>Conventions</h3> <ul style="list-style-type:disc;"> <li>The first track defines the sequence reference over which features are mapped </li> <li>A white circle over the start (or end) of a block indicates that the feature in its original reference does not start (or end) in that position but before (or after) </li> <li>A dashed line between blocks indicates that in the original reference the feature is connected and therefore a sequence insertion has occurred </li> <li>Color flags (blue/orange) between track titles and track features indicates feature provenance (blue for RCSB PDB and orange for third party resources) </li> </ul> <div style="height: 20px;"></div><a class="content-anchor" id="structure-summary-page--sequence-tab"></a> <h3>Structure Summary Page - Sequence Tab</h3> <p>In the Sequence Tab (e.g. <a href="/sequence/4z35" target="_blank" rel="noopener">4z35</a>) the Sequence Annotations Viewer will display the full range of available features (structural and biological annotations) and the alignments between Polymer Instances (chains) and <a href="https://www.uniprot.org" target="_blank" rel="noopener">UniProtKB</a> sequences. The select menu can be used to display the features for the different PDB Polymer Instances (chains) of the current Entry (Figure 1).</p> <div style="width:80%"><table><tr><td><a href="https://cdn.rcsb.org/rcsb-pdb/content/60103d1ab1afe64903398251/sa-fig1-jan24.png" data-toggle="lightbox" data-title="Figure 1: Sequence Annotations Viewer for PDB entry 4z35 showing features from the PDB entry (marked by blue vertical bar on the left) and features derived from UniProt, SCOP, PFam etc. (marked by orange vertical lines on the left). "><img class="img-responsive" src="https://cdn.rcsb.org/rcsb-pdb/content/60103d1ab1afe64903398251/sa-fig1-jan24.png" alt="Figure 1: Sequence Annotations Viewer for PDB entry 4z35 showing features from the PDB entry (marked by blue vertical bar on the left) and features derived from UniProt, SCOP, PFam etc. (marked by orange vertical lines on the left). "> </a></td></tr><tr><td class="content-img-caption" style="width:1170px;">Figure 1: Sequence Annotations Viewer for PDB entry 4z35 showing features from the PDB entry (marked by blue vertical bar on the left) and features derived from UniProt, SCOP, PFam etc. (marked by orange vertical lines on the left). </td></tr></table></div><div style="height: 20px;"></div><a class="content-anchor" id="structure-summary-page--main-tab"></a> <h3>Structure Summary Page - Main Tab</h3> <p>The Sequence Annotations Viewer in the Structure Summary Pages (e.g. <a href="/structure/4z35" target="_blank" rel="noopener">4z35</a>) displays the alignments between PDB Entity sequences and <a href="https://www.uniprot.org" target="_blank" rel="noopener">UniProtKB</a>. Additionally, it includes Entity features such as mutations and artifacts, and the different regions that has not been (or partially) observed at Instance level. The select menu can be used to change the reference (Entity/UniProtKB) over which features are mapped and displayed (Figure 2).</p> <div style="width:80%"><table><tr><td><a href="https://cdn.rcsb.org/rcsb-pdb/content/60103d1ab1afe64903398251/sa-fig2-jan24.png" data-toggle="lightbox" data-title="Figure 2: Sequence Annotations Viewer on the Structure Summary Page for PDB entry 4z35"><img class="img-responsive" src="https://cdn.rcsb.org/rcsb-pdb/content/60103d1ab1afe64903398251/sa-fig2-jan24.png" alt="Figure 2: Sequence Annotations Viewer on the Structure Summary Page for PDB entry 4z35"> </a></td></tr><tr><td class="content-img-caption" style="width:1170px;">Figure 2: Sequence Annotations Viewer on the Structure Summary Page for PDB entry 4z35</td></tr></table></div><div style="height: 20px;"></div><p>Disorder and disorded binding values are calculated based on sequence alone using IUPred (<a href="https://doi.org/10.1002/pro.3334" target="_blank">Dosztányi Z., 2018</a>) and ANCHOR (<a href="https://doi.org/10.1093/bioinformatics/btp518" target="_blank">Dosztányi, Z., et al., 2009</a>) algorithms, respectively. The reported disorder values for each residue range between 0 and 1, corresponding to its probability of being part of a disordered region. The lower the probability, the less likely a given residue is within disorder region. The 0.5 cutoff is used for coloring, blue more likely to be an ordered region, red - disordered.<br /><br />Hydropathy is calculated based on sequence alone using the Kyte-Doolittle hydrophobicity scale (<a href="https://doi.org/10.1016/0022-2836(82)90515-0" target="_blank">Kyte and Doolittle, 1982</a>).</p> <a class="content-anchor" id="feature-tooltips"></a> <h3>Feature Tooltips</h3> <p>Feature tooltips contain important information about feature positions in the current and original reference sequence. When the cursor is hovering over specific amino acid or sequence features, relevant tooltips are displayed top right corner of the Sequence Annotations Viewer (Figure 3)</p> <table><tr><td><img class="img-responsive" src="https://cdn.rcsb.org/rcsb-pdb/content/60103d1ab1afe64903398251/tooltip.png" alt="Figure 3: Tooltips that appear when the cursor is hovering over a specific feature in the Sequence Annotations Viewer"> </td></tr><tr><td class="content-img-caption" style="width:627px;">Figure 3: Tooltips that appear when the cursor is hovering over a specific feature in the Sequence Annotations Viewer</td></tr></table><div style="height: 20px;"></div><ul style="list-style-type:disc;"> <li> (i) Feature short name description </li> <li> (ii) Database source or software name used to obtain the feature. Color indicates its provenance (blue RCSB PDB and orange third party resources) </li> <li> (iii) Feature position in the current reference system </li> <li> (iv) PDB residue author Ids associated to the feature position </li> <li> (v) Feature source database/software name </li> <li> (vi) Feature original reference entry Id and positions </li> <li> (vii) Feature description </li> </ul> <div style="height: 20px;"></div><a class="content-anchor" id="for-developers"></a> <h3>For Developers</h3> <p>The Sequence Annotations Viewer (previously called Protein Feature View) is an Open Source project written in TypeScript. It is available at <a href="https://github.com/rcsb/rcsb-saguaro" target="_blank" rel="noopener">github.com</a></p> </div></div><br><hr><div class="item-info"><div>Please report any encountered broken links to <a href='mailto:info@rcsb.org'>info@rcsb.org</a></div><div>Last updated: 10/20/2024</div></div></div></div></div></div><div data-elastic-exclude><div class="hidden-print" id="footer_main"><div class="container" style="padding:0"><div class="row"><div class="col-md-6 col-sm-12" style="padding-left:0"> <div class="row"><div class="col-sm-4"><ul><li><span class="row_header">About</span></li><li><a href="/pages/about-us/index">About Us</a></li><li><a href="/pages/policies#References">Citing Us</a></li><li><a href="/pages/publications">Publications</a></li><li><a href="/pages/team">Team</a></li><li><a href="/pages/jobs">Careers</a></li><li><a href="/pages/policies">Usage & Privacy</a></li></ul></div><div class="col-sm-4" style="padding-left:0"><ul><li><span class="row_header">Support</span></li><li><a href="/pages/contactus">Contact Us</a></li><li><a href="/help">Help</a></li><li><a href="/docs/general-help/website-faq">Website FAQ</a></li><li><a href="/docs/general-help/glossary">Glossary</a></li><li><a href="https://status.rcsb.org/" target="_blank">Service Status</a></li></ul></div><div class="col-md-4 hidden-sm"></div></div></div><div class="col-md-6 col-sm-12" style="padding-left:5px"> <div class="row"><div class="col-sm-4"><p class="row_header">RCSB PDB is hosted by</p><div class="footerLogos"><hr><a href="https://radcollaboratory.rutgers.edu/"><img class="Rutgerslogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/rad-sm.png" alt="The Rutgers Artificial Intelligence and Data Science Collaboratory logo"></a><hr><a href="https://ucsd.edu/"><img class="UCSDlogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_UCSD-navy.png" alt="Uiversity of California San Diego logo"></a><a href="https://www.sdsc.edu/"><img class="SDSClogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_SDSC-black.png" alt="San Diego Supercomputer Center logo"></a><hr><a href="https://www.ucsf.edu/"><img class="UCSFlogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_UCSF.png" alt="University of California San Francisco Logo"></a></div></div><div class="col-sm-4"><p class="row_header">RCSB PDB is a member of the</p><div class="footerLogos"><span id="pdbmembers_footer"><hr><a href="https://www.wwpdb.org" target="_blank" rel="noopener"><img class="wwpdblogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_wwpdb.png" alt="wwPDB"></a><hr><a href="https://www.emdataresource.org" target="_blank" rel="noopener"><img id="emdatabanklogo_footer" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/EMDataResourcelogo.png" alt="EMDataResource"></a></span></div></div><div class="col-sm-4"><ul><li><span class="row_header">RCSB Partners</span></li><li><a href="https://nakb.org/" target="_blank" rel="noopener">Nucleic Acid Knowledgebase</a></li></ul><ul><li><span class="row_header"><a href="https://www.wwpdb.org/" target="_blank" rel="noopener" style="text-decoration: none; color: black">wwPDB Partners</a></span></li><li><a href="/">RCSB PDB</a></li><li><a href="https://www.ebi.ac.uk/pdbe/" target="_blank" rel="noopener">PDBe</a></li><li><a href="https://www.pdbj.org/" target="_blank" rel="noopener">PDBj</a></li><li><a href="https://bmrb.io/" target="_blank" rel="noopener">BMRB</a></li><li><a href="https://emdb-empiar.org/" target="_blank" rel="noopener">EMDB</a></li></ul></div></div></div></div></div></div><div id="footer_grant"><div class="container"><div class="row"><p>RCSB PDB Core Operations are funded by the <a href="http://www.nsf.gov/" target="_blank" rel="noopener">U.S. National Science Foundation</a> (DBI-2321666), the <a href="http://science.energy.gov/" target="_blank" rel="noopener">US Department of Energy</a> (DE-SC0019749), and the <a href="http://www.cancer.gov/" target="_blank" rel="noopener">National Cancer Institute</a>, <a href="http://www.niaid.nih.gov/" target="_blank" rel="noopener">National Institute of Allergy and Infectious Diseases</a>, and <a href="http://www.nigms.nih.gov/" target="_blank" rel="noopener">National Institute of General Medical Sciences</a> of the <a href="http://www.nih.gov/" target="_blank" rel="noopener">National Institutes of Health</a> under grant R01GM157729.</p></div></div></div><div id="jira-fdbck"></div></div></div></body></html>

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