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id="618271c92a7d828464a7d146" onclick="toggle("618271c92a7d828464a7d146")"><table><tr><td style="padding-left: 4px">Exploring a 3D Structure</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph618271c92a7d828464a7d146"></span></td></tr></table></div><div class="item hidden" id="618274c904fb9835c6ae189a"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/overview">Overview</a></td></tr></table></div><div class="item hidden" id="618271f904fb9835c6ae1892"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/structure-summary-page">Structure Summary Page</a></td></tr></table></div><div class="item hidden" id="6182729704fb9835c6ae1893"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/structure">Structure</a></td></tr></table></div><div class="item hidden" id="618272c004fb9835c6ae1894"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/exploring-a-3d-structure/annotations">Annotations</a></td></tr></table></div><div class="item hidden" id="618272e004fb9835c6ae1895"><table><tr><td class="title" style="padding-left: 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="6256b2b3b4396e45e97bf3de" onclick="toggle("6256b2b3b4396e45e97bf3de")"><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 href="/docs/grouping-structures/overview-grouping-structures">Overview: Grouping Structures</a></td></tr></table></div><div class="item hidden" id="6081c10aec901916050494be"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/grouping-structures/sequence-based-clustering">Sequence-based Clustering</a></td></tr></table></div><div class="item hidden" id="6256b3269c3931864b07285b"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/grouping-structures/grouping-search-results">Grouping Search Results</a></td></tr></table></div><div class="item hidden" id="6256b35e9c3931864b07285c"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/grouping-structures/group-summary-pages">Group Summary Pages</a></td></tr></table></div><div class="item hidden" id="6364336066d6046810db7f11"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/grouping-structures/explore-sequence-alignments-in-3d">Explore Sequence Alignments in 3D</a></td></tr></table></div><div class="group show" id="5fd3e3a6eb210c2c5632d098" onclick="toggle("5fd3e3a6eb210c2c5632d098")"><table><tr><td style="padding-left: 4px">3D Viewers</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph5fd3e3a6eb210c2c5632d098"></span></td></tr></table></div><div class="group hidden" id="5f98cc9614cc37a34de620ea" onclick="toggle("5f98cc9614cc37a34de620ea")"><table><tr><td style="padding-left: 24px">Mol*</td><td><span 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id="5ee1192f25aa7b208a9fe3a3"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/3d-viewers/mol*/managing-the-display">Managing the Display</a></td></tr></table></div><div class="item hidden" id="5ee13ac17f50f44e6aa4fb1f"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/3d-viewers/mol*/common-actions">Common Actions</a></td></tr></table></div><div class="item hidden" id="5ee231607f50f44e6aa4fb20"><table><tr><td class="title" style="padding-left: 44px"><a href="/docs/3d-viewers/mol*/faqs-scenarios">FAQs/Scenarios</a></td></tr></table></div><div class="item hidden" 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="5fd3e3f4eb210c2c56332c65" onclick="toggle("5fd3e3f4eb210c2c56332c65")"><table><tr><td style="padding-left: 4px">Sequence Viewers</td><td><span class="glyphicon glyphicon-triangle-bottom" id="glyph5fd3e3f4eb210c2c56332c65"></span></td></tr></table></div><div class="item hidden" id="60103d1ab1afe64903398251"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/sequence-viewers/sequence-annotations-viewer">Sequence Annotations Viewer</a></td></tr></table></div><div class="item hidden" id="60342ff52087e87def0d0b09"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/sequence-viewers/sequence-annotations-in-3d">Sequence Annotations in 3D</a></td></tr></table></div><div class="item hidden" 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="item hidden" id="60182dc1ecb9a74be53123aa"><table><tr><td class="title" style="padding-left: 24px"><a href="/docs/sequence-viewers/protein-sequence-alignment-view">Protein Sequence Alignment View</a></td></tr></table></div><div class="group show" id="60132e62aeeea33d3f095fa8" onclick="toggle("60132e62aeeea33d3f095fa8")"><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="601024f3244a4309df5d6630" 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Models</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">Programmatic Access</h5><h1>File Download Services</h1><div><div style="padding-left:20px;">● <a href="#the-pdb-archive">The PDB archive</a></div> <div style="padding-left:40px;">○ <a href="#file-access-urls-">File Access URLs </a></div> <div style="padding-left:40px;">○ <a href="#automated-download-of-data">Automated download of data</a></div> <div style="padding-left:40px;">○ <a href="#major-directories-in-the-pdb-archive">Major directories in the PDB archive</a></div> <div style="padding-left:20px;">● <a href="#other-downloads-offered-by-rcsb-pdb">Other downloads offered by RCSB PDB</a></div> <div style="padding-left:40px;">○ <a href="#pdb-entry-files">PDB entry files</a></div> <div style="padding-left:40px;">○ <a href="#small-molecule-files">Small molecule files</a></div> <div style="padding-left:40px;">○ <a href="#experimental-data-files-and-3dem-maps">Experimental data files and 3DEM maps</a></div> <div style="padding-left:40px;">○ <a href="#sequence-data">Sequence data</a></div> <div style="padding-left:40px;">○ <a href="#sequence-clusters-data">Sequence clusters data</a></div> <div style="padding-left:40px;">○ <a href="#holdings-data">Holdings data</a></div> <div style="padding-left:40px;">○ <a href="#chemical-component-dictionary-ccd-data">Chemical Component Dictionary (CCD) Data</a></div> <a class="content-anchor" id="the-pdb-archive"></a> <h2>The PDB archive</h2> <p>Searches and reports performed on this RCSB PDB website utilize data from the PDB archive. The PDB archive is maintained by the <a href="https://www.wwpdb.org/" target="_blank" rel="noopener" >wwPDB</a> at the main archive, files.wwpdb.org (<a href="https://www.wwpdb.org/ftp/pdb-ftp-sites" target="_blank" rel="noopener" >data download details</a>) and the versioned archive, files-versioned.wwpdb.org (<a target="_blank" rel="noopener" href="https://www.wwpdb.org/ftp/pdb-versioned-ftp-site">versioning details</a>). Since February 01 2023, the wwPDB enriches PDB entries with additional annotation and distributes the latest versions of each entry via next generation archive (NextGen) accessible at <a href="https://files-nextgen.wwpdb.org" target="_blank">files-nextgen.wwpdb.org</a>.</p> <p>In addition to experimental structures, the PDB archive includes structures determined by integrative and hybrid structure determination methods (IHM). Users can access and download IHM structures and associated data at <a href="https://files.wwpdb.org/pub/pdb_ihm/" target="_blank">files.wwpdb.org/pub/pdb_ihm/</a>.</p> <p>All data are available via the <a href="https://files.wwpdb.org/" target="_blank">HTTPS</a> protocol. Note that the FTP protocol is no longer supported. See the <a href="/news/636151b266d6046810db7f0f">announcement</a>.</p> <p>RCSB PDB additionally hosts the archive as part of the Registry of Open Data on Amazon Web Services (AWS) at <a href="https://s3.rcsb.org/" target="_blank">https://s3.rcsb.org</a> following the same directory structure.</p> <a class="content-anchor" id="file-access-urls-"></a> <h3>File Access URLs</h3> <p>DNS names are required for programmatic access to PDB archive downloads:</p> <ul style="list-style-type:disc;"> <li>HTTPS: <a href="https://files.rcsb.org/" target="_blank">https://files.wwpdb.org</a></li> <li>RSYNC: rsync://rsync.rcsb.org</li> </ul> <div style="height: 20px;"></div><a class="content-anchor" id="automated-download-of-data"></a> <h3>Automated download of data</h3> <p>The URLs in this document are useful for scripted downloads using utilities such as <a href="https://en.wikipedia.org/wiki/Wget" target="_blank" rel="noopener" >wget</a>. For instance you can consider using the <a href="/docs/programmatic-access/batch-downloads-with-shell-script">batch downloads shell script</a>.</p> <p>The RCSB PDB also provides <a target="_blank" rel="noopener" href="https://rsync.samba.org/">rsync</a> capabilities, useful when maintaining full copies of the archive. These are 2 example scripts to assist in the automated download of data with rsync:</p> <ul style="list-style-type:disc;"> <li><a href="ftp://snapshots.rcsb.org/rsyncSnapshots.sh">ftp://snapshots.rcsb.org/rsyncSnapshots.sh</a> To make a local copy of an annual snapshot or sections of the snapshot. This script is annotated to assist in downloading only sections of the archive.</li> <li><a href="https://files.wwpdb.org/pub/pdb/software/rsyncPDB.sh">https://files.wwpdb.org/pub/pdb/software/rsyncPDB.sh</a> To copy the current contents of the entire archive</li> </ul> <div style="height: 20px;"></div><p>Additional information on obtaining and maintaining copies of the entire PDB archive or certain portions of it is available at <a href="https://www.wwpdb.org/downloads.html" target="_blank" rel="noopener" >https://www.wwpdb.org/downloads.html</a>.</p> <a class="content-anchor" id="major-directories-in-the-pdb-archive"></a> <h3>Major directories in the PDB archive</h3> <p>The directory <a href="https://files.wwpdb.org/pub/pdb" target="_blank" rel="noopener" >pub/pdb</a> is the entry directory for the PDB archive downloads.</p> <p>Some general notes:</p> <ul style="list-style-type:disc;"> <li>Entry files are date-stamped to show the date they were released </li> <li>Entries are grouped by the middle two characters of the 4-character PDB identifier. For example, entry file pdb100d.ent can be found in <a href="https://files.wwpdb.org/pub/pdb/data/structures/divided/pdb/00/pdb100d.ent.gz" target="_blank" rel="noopener" >pub/pdb/data/structures/divided/pdb/00/pdb100d.ent.gz</a></li> <li>The two letter naming convention for structure holdings is retained for the directories within <b>/pub/pdb/data/structures/divided</b> and <b>/pub/pdb/data/structures/divided/obsolete</b> but not for the directories within <b>/pub/pdb/data/structures/all</b>, which contain the structure holdings in undivided layout.</li> <li>PDB entries are available in PDB, mmCIF, and PDBML/XML format. </li> <li>Only UNIX <b>compressed files</b> are supported for coordinates, structure factors, and restraints.</li> </ul> <div style="height: 20px;"></div><p>For information about large structures that cannot be represented in the legacy PDB file format see <a href="/docs/general-help/structures-without-legacy-pdb-format-files" target="_blank">here</a>.</p> <table class="content-resources"> <tbody> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/" target="_blank">/pub/pdb/data/assemblies/mmCIF</a> </td> <td>Biological assembly coordinate files in mmCIF format</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/data/biounit/PDB" target="_blank">/pub/pdb/data/biounit/PDB</a> </td> <td>Biological assembly coordinate files in PDB format</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/data/monomers" target="_blank">/pub/pdb/data/monomers</a> </td> <td>PDB Chemical Component Dictionary and other info on monomers</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/data/status" target="_blank">/pub/pdb/data/status</a> </td> <td>Details of entries on hold and in processing</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/data/structures/all" target="_blank">/pub/pdb/data/structures/all</a> </td> <td>Analogous to the divided directory, containing pdb, mmCIF, nmr_restraint, and structure_factors directories, with symbolic links to files in the divided subdirectories. In the ./all directory, files are not divided into two-letter directories, however.</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/data/structures/divided" target="_blank">/pub/pdb/data/structures/divided</a> </td> <td>This is the entry point for a user finding a structure. This directory contains the current PDB, in pdb, mmCIF, XML, nmr_restraint, and structure_factors directories, with the files divided according to a two letter organization. Entries are grouped by the middle two characters of the ident code. For example, entry file pdb1abc.ent can be found in pub/pdb/data/structures/divided/pdb/ab</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/data/structures/models" target="_blank">/pub/pdb/data/structures/models</a> </td> <td>Theoretical model files that are maintained separately from the main archive</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/data/structures/obsolete" target="_blank">/pub/pdb/data/structures/obsolete</a> </td> <td>Structures and associated data files no longer part of the archive</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/derived_data" target="_blank">/pub/pdb/derived_data</a> </td> <td>Plain text files that list information derived from all PDB entries, such as all PDB sequences in FASTA format.</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/doc" target="_blank">/pub/pdb/doc</a> </td> <td>Documentation, including file format descriptions and RCSB PDB Newsletters</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb/validation_reports/" target="_blank">/pub/pdb/validation_reports</a> </td> <td>Validation reports files in mmCIF, PDF and XML formats and supporting data</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb_ihm/data/entries/" target="_blank">/pub/pdb_ihm/data/entries/</a> </td> <td>Structures determined by integrative and hybrid structure determination methods (IHM) and associated data files</td> </tr> <tr> <td> <a href="https://files.wwpdb.org/pub/pdb_ihm/holdings/" target="_blank">/pub/pdb_ihm/holdings/</a> </td> <td>Current PDB-IHM holdings, released IHM structures last modified dates, unreleased IHM entries</td> </tr> </tbody> </table> <div style="height: 20px;"></div> <a class="content-anchor" id="other-downloads-offered-by-rcsb-pdb"></a> <h2>Other downloads offered by RCSB PDB</h2> <p>Some of the http links above are also available in a short style (e.g. <a href="https://files.rcsb.org/download/4hhb.cif.gz">/download/4hhb.cif.gz</a>). Additionally, for the short style links 2 URLs are available:</p> <ul style="list-style-type:disc;"> <li><b>view</b>: The HTTP/HTTPS response headers to the client are set with: Content-Type: text/plain</li> <li><b>download</b>: The HTTP/HTTPS response headers to the client are set with: Content-Type: application/octet-stream and Content-Transfer-Encoding: binary</li> </ul> <div style="height: 20px;"></div><a class="content-anchor" id="pdb-entry-files"></a> <h3>PDB entry files</h3> <p>PDB entry files are available in several file formats (PDB, PDBx/mmCIF, XML, BinaryCIF), compressed or uncompressed, and with an option to download a file containing only "header" information (summary data, no coordinates).</p> <table class="table table-bordered"> <thead> <tr> <th>File Format</th> <th>Action</th> <th>Storage Compression</th> <th>Example URL</th> </tr> </thead> <tbody> <tr> <td>Biological Assembly File in PDB</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/1hh3.pdb1" target="_blank" rel="noopener">https://files.rcsb.org/download/1hh3.pdb1</a></td> </tr> <tr> <td>Biological Assembly File in PDB</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/1hh3.pdb1.gz" target="_blank" rel="noopener">https://files.rcsb.org/download/1hh3.pdb1.gz</a></td> </tr> <tr> <td>Biological Assembly File in PDBx/mmCIF</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/5a9z-assembly1.cif" target="_blank" rel="noopener">https://files.rcsb.org/download/5a9z-assembly1.cif</a></td> </tr> <tr> <td>Biological Assembly File in PDBx/mmCIF</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/5a9z-assembly1.cif.gz" target="_blank" rel="noopener">https://files.rcsb.org/download/5a9z-assembly1.cif.gz</a></td> </tr> <tr> <td>PDB</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/4hhb.pdb.gz" target="_blank" rel="noopener">https://files.rcsb.org/download/4hhb.pdb.gz</a></td> </tr> <tr> <td>PDB</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/4hhb.pdb" target="_blank" rel="noopener">https://files.rcsb.org/download/4hhb.pdb</a></td> </tr> <tr> <td>PDBx/BinaryCIF</td> <td>Download</td> <td>Compressed</td> <td><a href="https://models.rcsb.org/4hhb.bcif.gz" target="_blank" rel="noopener">https://models.rcsb.org/4hhb.bcif.gz</a></td> </tr> <tr> <td>PDBx/BinaryCIF</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://models.rcsb.org/4hhb.bcif" target="_blank" rel="noopener">https://models.rcsb.org/4hhb.bcif</a></td> </tr> <tr> <td>PDBx/mmCIF</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/4hhb.cif.gz" target="_blank" rel="noopener">https://files.rcsb.org/download/4hhb.cif.gz</a></td> </tr> <tr> <td>PDBx/mmCIF</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/4hhb.cif" target="_blank" rel="noopener">https://files.rcsb.org/download/4hhb.cif</a></td> </tr> <tr> <td>XML</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/4hhb.xml.gz" target="_blank" rel="noopener">https://files.rcsb.org/download/4hhb.xml.gz</a></td> </tr> <tr> <td>XML</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/4hhb.xml" target="_blank" rel="noopener">https://files.rcsb.org/download/4hhb.xml</a></td> </tr> <tr> <td>XML (header only)</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/4hhb-noatom.xml.gz" target="_blank" rel="noopener">https://files.rcsb.org/download/4hhb-noatom.xml.gz</a></td> </tr> <tr> <td>XML (header only)</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/4hhb-noatom.xml" target="_blank" rel="noopener">https://files.rcsb.org/download/4hhb-noatom.xml</a></td> </tr> <tr> <td>Biological Assembly File in PDB</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/view/1hh3.pdb1" target="_blank" rel="noopener">https://files.rcsb.org/view/1hh3.pdb1</a></td> </tr> <tr> <td>Biological Assembly File in PDBx/mmCIF</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/view/5a9z-assembly1.cif" target="_blank" rel="noopener">https://files.rcsb.org/view/5a9z-assembly1.cif</a></td> </tr> <tr> <td>PDB</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/view/4hhb.pdb" target="_blank" rel="noopener">https://files.rcsb.org/view/4hhb.pdb</a></td> </tr> <tr> <td>PDB (header only)</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/header/4hhb.pdb" target="_blank" rel="noopener">https://files.rcsb.org/header/4hhb.pdb</a></td> </tr> <tr> <td>PDBx/mmCIF</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/view/4hhb.cif" target="_blank" rel="noopener">https://files.rcsb.org/view/4hhb.cif</a></td> </tr> <tr> <td>PDBx/mmCIF (header only)</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/header/4hhb.cif" target="_blank" rel="noopener">https://files.rcsb.org/header/4hhb.cif</a></td> </tr> <tr> <td>XML (header only)</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/view/4hhb-noatom.xml" target="_blank" rel="noopener">https://files.rcsb.org/view/4hhb-noatom.xml</a></td> </tr> </tbody> </table> <div style="height: 20px;"></div> <a class="content-anchor" id="small-molecule-files"></a> <h3>Small molecule files</h3> <p>Small molecule files, including the ligands/chemical components maintained in the Chemical Component Dictionary and the Biologically Interesting Molecule Reference Dictionary (BIRD) are available in multiple formats.</p> <table class="table table-bordered"> <thead> <tr> <th>Type</th> <th>Format</th> <th>Action</th> <th>Example URL</th> </tr> </thead> <tbody> <tr> <td>BIRD atom representation</td> <td>CIF</td> <td>Download</td> <td><a href="https://files.rcsb.org/birds/download/PRDCC_000001.cif" target="_blank">https://files.rcsb.org/birds/download/PRDCC_000001.cif</a></td> </tr> <tr> <td>BIRD definition</td> <td>CIF</td> <td>Download</td> <td><a href="https://files.rcsb.org/birds/download/PRD_000001.cif" target="_blank">https://files.rcsb.org/birds/download/PRD_000001.cif</a></td> </tr> <tr> <td>Definition</td> <td>CIF</td> <td>Download</td> <td><a href="https://files.rcsb.org/ligands/download/HEM.cif" target="_blank">https://files.rcsb.org/ligands/download/HEM.cif</a></td> </tr> <tr> <td>Ideal coordinates</td> <td>MOL2</td> <td>Download</td> <td><a href="https://files.rcsb.org/ligands/download/HEM_ideal.mol2" target="_blank">https://files.rcsb.org/ligands/download/HEM_ideal.mol2</a></td> </tr> <tr> <td>Ideal coordinates</td> <td>SDF</td> <td>Download</td> <td><a href="https://files.rcsb.org/ligands/download/HEM_ideal.sdf" target="_blank">https://files.rcsb.org/ligands/download/HEM_ideal.sdf</a></td> </tr> <tr> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td></td> <td></td> <td></td> <td></td> </tr> <tr> <td>BIRD atom representation</td> <td>CIF</td> <td>View</td> <td><a href="https://files.rcsb.org/birds/view/PRDCC_000001.cif" target="_blank">https://files.rcsb.org/birds/view/PRDCC_000001.cif</a></td> </tr> <tr> <td>BIRD definition</td> <td>CIF</td> <td>View</td> <td><a href="https://files.rcsb.org/birds/view/PRD_000001.cif" target="_blank">https://files.rcsb.org/birds/view/PRD_000001.cif</a></td> </tr> <tr> <td>Chemical Component Instance</td> <td>SDF</td> <td>View</td> <td><a href="https://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=sdf" target="_blank">https://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=sdf</a></td> </tr> <tr> <td>Chemical Component Instance</td> <td>MOL</td> <td>View</td> <td><a href="https://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=mol" target="_blank">https://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=mol</a></td> </tr> <tr> <td>Chemical Component Instance</td> <td>MOL2</td> <td>View</td> <td><a href="https://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=mol2" target="_blank">https://models.rcsb.org/v1/4hhb/ligand?auth_asym_id=A&auth_seq_id=142&encoding=mol2</a></td> </tr> <tr> <td>Definition</td> <td>CIF</td> <td>View</td> <td><a href="https://files.rcsb.org/ligands/view/HEM.cif" target="_blank">https://files.rcsb.org/ligands/view/HEM.cif</a></td> </tr> <tr> <td>Ideal coordinates</td> <td>MOL2</td> <td>View</td> <td><a href="https://files.rcsb.org/ligands/view/HEM_ideal.mol2" target="_blank">https://files.rcsb.org/ligands/view/HEM_ideal.mol2</a></td> </tr> <tr> <td>Ideal coordinates</td> <td>SDF</td> <td>View</td> <td><a href="https://files.rcsb.org/ligands/view/HEM_ideal.sdf" target="_blank">https://files.rcsb.org/ligands/view/HEM_ideal.sdf</a></td> </tr> </tbody> </table> <div style="height: 20px;"></div> <a class="content-anchor" id="experimental-data-files-and-3dem-maps"></a> <h3>Experimental data files and 3DEM maps</h3> <p>This table includes structure factors, NMR constraints, chemical shifts, electron density maps and map coefficient files.</p> <table class="table table-bordered"> <thead> <tr> <th>File Format</th> <th>Action</th> <th>Storage Compression</th> <th>Example URL</th> </tr> </thead> <tbody> <tr> <td>Chemical Shifts</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/2n2z_cs.str.gz">https://files.rcsb.org/download/2n2z_cs.str.gz</a></td> </tr> <tr> <td>Chemical Shifts</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/2n2z_cs.str">https://files.rcsb.org/download/2n2z_cs.str</a></td> </tr> <tr> <td>Chemical Shifts</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/view/2n2z_cs.str">https://files.rcsb.org/view/2n2z_cs.str</a></td> </tr> <tr> <td>Combined NMR data (NEF)</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/pub/pdb/data/structures/divided/nmr_data/e5/1e52_nmr-data.nef.gz">https://files.rcsb.org/pub/pdb/data/structures/divided/nmr_data/e5/1e52_nmr-data.nef.gz</a></td> </tr> <tr> <td>Combined NMR data (NMR-STAR)</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/pub/pdb/data/structures/divided/nmr_data/e5/1e52_nmr-data.str.gz">https://files.rcsb.org/pub/pdb/data/structures/divided/nmr_data/e5/1e52_nmr-data.str.gz</a></td> </tr> <tr> <td>Structure Factors</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/1btn-sf.cif.gz">https://files.rcsb.org/download/1btn-sf.cif.gz</a></td> </tr> <tr> <td>Structure Factors</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/1btn-sf.cif">https://files.rcsb.org/download/1btn-sf.cif</a></td> </tr> <tr> <td>Structure Factors</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/view/1btn-sf.cif">https://files.rcsb.org/view/1btn-sf.cif</a></td> </tr> <tr> <td>Electron Density 2Fo-Fc & Fo-Fc Map (might be downsampled) - BinaryCIF format</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://maps.rcsb.org/x-ray/6dil/cell/">https://maps.rcsb.org/x-ray/6dil/cell/</a></td> </tr> <tr> <td>NMR Restraints</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/108d.mr.gz">https://files.rcsb.org/download/108d.mr.gz</a> </td> </tr> <tr> <td>NMR Restraints</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/108d.mr">https://files.rcsb.org/download/108d.mr</a></td> </tr> <tr> <td>NMR Restraints</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/view/108d.mr">https://files.rcsb.org/view/108d.mr</a></td> </tr> <tr> <td>NMR Restraints v2</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/download/108d_mr.str.gz">https://files.rcsb.org/download/108d_mr.str.gz</a></td> </tr> <tr> <td>NMR Restraints v2</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/download/108d_mr.str">https://files.rcsb.org/download/108d_mr.str</a></td> </tr> <tr> <td>NMR Restraints v2</td> <td>View</td> <td>Uncompressed</td> <td><a href="https://files.rcsb.org/view/108d_mr.str">https://files.rcsb.org/view/108d_mr.str</a></td> </tr> </tbody> </table> <div style="height: 20px;"></div> <a class="content-anchor" id="sequence-data"></a> <h3>Sequence data</h3> <p>Sequence data in FASTA format (full deposited sequence as in SEQRES records).</p> <p>Please note that the FASTA download service at URL <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">/pdb/download/downloadFastaFiles.do?structureIdList=4hhb&compressionType=uncompressed</code>has been discontinued. Users will need to migrate to the new endpoints below. Note that the output of the new endpoints are per entity (with chain identifiers provided in header) instead of per chain.</p> <table class="table table-bordered"> <tbody> <tr> <td>FASTA sequences per PDB entry</td> <td>Download</td> <td>Uncompressed</td> <td><a href="/fasta/entry/4HHB/download">/fasta/entry/4HHB/download</a></td> </tr> <tr> <td>FASTA sequence per polymer entity (identified by <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;"><pdb_id>_<entity_id></code>)</td> <td>Download</td> <td>Uncompressed</td> <td><a href="/fasta/entity/4HHB_1/download">/fasta/entity/4HHB_1/download</a></td> </tr> <tr> <td>FASTA sequence per polymer entity instance (chain) (identified by <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;"><pdb_id>.<asym_id></code>, please note this is the label_asym_id and not the author chain id)</td> <td>Download</td> <td>Uncompressed</td> <td><a href="/fasta/chain/4HHB.A/download">/fasta/chain/4HHB.A/download</a></td> </tr> <tr> <td>Sequences in FASTA format for all entries in the PDB archive</td> <td>Download</td> <td>Compressed</td> <td><a href="https://files.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt.gz">https://files.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt.gz</a></td> </tr> </tbody> </table> <div style="height: 20px;"></div> <a class="content-anchor" id="sequence-clusters-data"></a> <h3>Sequence clusters data</h3> <p>Results of the weekly clustering of protein sequences in the PDB by<a href="https://github.com/soedinglab/MMseqs2" target="_blank" rel="noopener" > MMseqs2</a> at 30%, 40%, 50%, 70%, 90%, 95%, and 100% sequence identity. Note that these files use polymer entity identifiers, instead of chain identifiers to avoid redundancy. The files are plain text with one cluster per line, sorted from largest cluster to smallest.</p> <table class="table table-bordered"> <thead> <tr> <th>File</th> <th>Type</th> <th>Storage Compression</th> <th>URL</th> </tr> </thead> <tbody> <tr> <td>Sequence clusters at <identity> % sequence identity clustering</td> <td>Download</td> <td>Uncompressed</td> <td>https://cdn.rcsb.org/resources/sequence/clusters/clusters-by-entity-<identity>.txt</td> </tr> </tbody> </table> <div style="height: 20px;"></div> <a class="content-anchor" id="holdings-data"></a> <h3>Holdings data</h3> <p>PDB id holdings data in json format. For more information, see the <a href="https://data.rcsb.org/redoc/index.html">data API documentation</a>.</p> <table class="table table-bordered"> <thead> <tr> <th>File</th> <th>Type</th> <th>Storage Compression</th> <th>URL</th> </tr> </thead> <tbody> <tr> <td>All current PDB ids</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://data.rcsb.org/rest/v1/holdings/current/entry_ids">https://data.rcsb.org/rest/v1/holdings/current/entry_ids</a></td> </tr> <tr> <td>All unreleased PDB ids</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://data.rcsb.org/rest/v1/holdings/unreleased/entry_ids">https://data.rcsb.org/rest/v1/holdings/unreleased/entry_ids</a></td> </tr> <tr> <td>All removed PDB ids (obsoleted entries or theoretical models)</td> <td>Download</td> <td>Uncompressed</td> <td><a href="https://data.rcsb.org/rest/v1/holdings/removed/entry_ids">https://data.rcsb.org/rest/v1/holdings/removed/entry_ids</a></td> </tr> </tbody> </table> <div style="height: 20px;"></div> <a class="content-anchor" id="chemical-component-dictionary-ccd-data"></a> <h3>Chemical Component Dictionary (CCD) Data</h3> <p>A subset of properties is provided for all components from the <a href="https://www.wwpdb.org/data/ccd" target="_blank">Chemical Component Dictionary (CCD)</a> which describes chemical properties of all molecules in the PDB archive. The atom file (cca.bcif) provides the following CIF columns: <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">atom_id</code>, <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">comp_id</code>, <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">charge</code>, and <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">pdbx_stereo_config</code>. The bond file (ccb.bcif) provides the following CIF columns: <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">atom_id_1</code>, <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">atom_id_2</code>, <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">comp_id</code>, <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">molstar_protonation_variant</code>, <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">pdbx_aromatic_flag</code>, <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">pdbx_stereo_config</code>, and <code style="padding: 2px 4px;font-size: 90%;color: #c7254e;background-color: #f9f2f4;border-radius: 4px;">value_order</code>.<br /><br />This data can be used by the <a href="https://molstar.org/docs/data-access-tools/model-server/">Mol* ModelServer</a>.</p> <table class="table table-bordered"> <thead> <tr> <th>File</th> <th>Format</th> <th>Action</th> <th>URL</th> </tr> </thead> <tbody> <tr> <td>Chemical Component Atom Data</td> <td>BinaryCIF</td> <td>Download</td> <td><a href="https://models.rcsb.org/cca.bcif" target="_blank">https://models.rcsb.org/cca.bcif</a></td> </tr> <tr> <td>Chemical Component Bond Data</td> <td>BinaryCIF</td> <td>Download</td> <td><a href="https://models.rcsb.org/ccb.bcif" target="_blank">https://models.rcsb.org/ccb.bcif</a></td> </tr> </tbody> </table> <div style="height: 20px;"></div> </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: 11/5/2024</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="http://www.rutgers.edu/"><img class="Rutgerslogo" src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/Logo_Rutgers-2024.png" alt="Rutgers University 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; 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