196 lines
24 KiB
Text
196 lines
24 KiB
Text
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<title>7MXD: Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in complex with HIV-1 Env</title>
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<meta name="description" content="3BNC117 antibody heavy chain3BNC117 antibody light chainEnvelope glycoprotein gp120Envelope glycoprotein gp41J038 antibody heavy chainJ038 antibody light chain2-acetamido-2-deoxy-beta-D-glucopyranose">
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<meta name="keywords" content="3BNC117 antibody heavy chain, 3BNC117 antibody light chain, Envelope glycoprotein gp120, Envelope glycoprotein gp41, J038 antibody heavy chain, J038 antibody light chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, PHOSPHATE ION, alpha-D-mannopyranose, beta-D-mannopyranose, MMDB, Protein structure, protein interaction">
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<table cellspacing="0" id="mmdb_logo_links" cellpadding="0" width="100%"><tr><td><a class="ncbi_home_logo" href="/" alt="NBI HOME Logo">NCBI</a><div class="NLMLogo">National Center for<br/>Biotechnology Information</div></td><td class="titletext" align="left"><!--a href="/Structure/MMDB/mmdb.shtml"--><img border=0 src="/Structure/MMDB/strbanner.jpg" alt="7MXD - NCBI MMDB Logo"><!--/a--></td><td style="padding-bottom:1em;vertical-align:bottom"><form id="mmdbsearch" method="get" name="mmdbsearch" action="/Structure/pdb/" style="margin:0;padding:0;vertical-align: bottom;"><div class="mmdb-search-holder" style="height:100%;line-height:100%"><input accesskey="S" id="mmdb-search-box" type="search" name="uid" placeholder="Enter PDB ID or MMDB ID" value = "" aria-describedby="mmdb-search-uid" title="Enter PDB ID or MMDB ID"><button id="mmdb-search-button" class="__button mmdb-search-button" style="height:100%;line-height:100%;margin-right:-3px;" type="submit">Search</button></div></form></td></tr></table>
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<!-- StructureInfo start -->
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<section data-section="infor" id="structure-infor-section"><h1 class="structure-title" data-mmdbid="213628" data-pdbid="7MXD" id="structure-title"><a class="link title-pdbid" href="http://www.rcsb.org/pdb/explore/explore.do?structureId=7MXD" style="font-weight:600;margin:0;">7MXD: </a><span>Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in complex with HIV-1 Env</span></h1>
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<div class="floatClear" id="infor-detail"><div class="reference_section" data-pmids="35319830" id="reference-section"></div>
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<div class="property_section"><form action="/Structure/mmdb/mmdbsrv.cgi" method="post" id="reloadform" name="reloadform" style="margin:0;padding:0"><input type="hidden" name="uid" value="213628"/></form><table border="0" cellpadding="4" cellspacing="4"><tr><td class="H4 pdbid-download">PDB ID: </td>
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<td><a id="pdb_id_link" class="link" href="http://www.rcsb.org/pdb/explore/explore.do?structureId=7MXD" title="PDB ID">7MXD</a><a id="download-pdb-file" class="__button" tabindex="-1" href="https://files.rcsb.org/download/7MXD.pdb" title="Download PDB file" download="7MXD.pdb">Download</a><a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#MmdbsrvStructureViewDataSetPDBdataset" title="-click to see help"></a></td>
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</tr>
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<tr><td class="H4 property-name">MMDB ID: </td>
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<td style="font-weight:bold"><span class="info-item">213628</span> <a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#MmdbsrvRecordIdentifiers" title="-click to see help"></a></td>
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</tr>
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<tr><td class="H4 property-name">PDB Deposition Date: </td>
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<td><span id="depositionterm" style="padding-left: 0.2em;">2021/5/19<a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#MmdbsrvDeposited" title="-click to see help"></a></span></td>
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</tr>
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<tr><td class="H4 property-name">Updated in MMDB: </td>
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<td class="text" nowrap><span id="mmdb_updated" style="padding-left:0.2em">2022/06</span><a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#MmdbsrvUpdatedInMMDB" title="-click to see help"></a></td>
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</tr>
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<tr><td class="H4 property-name">Experimental Method: </td>
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<td class="TEXT" nowrap><div id="expmethod"><span title="electron microscopy" class="info-item">electron microscopy</span> <a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#MmdbsrvExperimentalMethod" title="-click to see help"></a></div></td>
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</tr>
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<tr><td class="H4 property-name">Resolution: </td>
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<td class="TEXT" id="resolution" nowrap>3.4 Å<a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#SearchFieldResolution" title="-click to see help"></a></td>
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</tr>
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<tr><td class="H4 property-name">Source Organism: </td>
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<td class="text"><div id="taxonomy"><div id="taxonomyterm"><span id="multitaxon" style="display:inline-block"><span id="taxword" title="Human immunodeficiency virus 1">Human immunodeficiency virus 1</span><span arr="down" class="taxdrop_arrow">▼</span></span><a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#MmdbsrvTaxonomy" title="-click to see help"></a></div>
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<div class="menupop" id="taxonomycontent"><table cellpadding="0" cellspacing="0" width="300"><tr><th width="50%">Taxonomy</th>
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<th width="50%">Molecule</th>
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<tr><td><a class="link taxcell" href="//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=11676" style="text-decoration:underline;">Human immunodeficiency virus 1</a></td>
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<td>A, F, G, B, I, H</td>
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</tr>
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<tr><td><a class="link taxcell" href="//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=9606" style="text-decoration:underline;">Homo sapiens</a></td>
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<td>C, D, J, K, S, U</td>
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</tr>
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<tr><td><a class="link taxcell" href="//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=9544" style="text-decoration:underline;">Macaca mulatta</a></td>
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<td>X, Y</td>
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</tr>
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</table></div>
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</div></td>
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</tr>
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<tr><td class="H4 property-name">Similar Structures: </td>
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<td><div id="vast-button-holder" style="width:100%;overflow:hidden;"><button class="__button" id="vast_button" type="submit">VAST+</button>
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<a class="help-img" href="/Structure/vastplus/docs/vastplus_help.html" title="-click to see help"></a></div></td>
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<tr><td colspan="2" style="text-align: center"><button class="__button" id="download_sequence" type="submit">Download sequence data</button>
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<a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#MmdbsrvDownaloadSequenceMMDB" title="-click to see help"></a></td></tr>
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</table>
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</div>
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</div>
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</section>
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<!-- end of StructureInfo -->
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<tr><td align="center">
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<!-- start annotations -->
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<div align="center" id="annotblock" style="margin-top:0.8em;"><div class="formbox" id="authormethod"><div id="bublock0"><div class="biotext" id="bublock0_unit_name">Biological Unit for 7MXD: 14-meric; determined by author<a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#MmdbsrvBiologicalUnit" title="-click to see help"></a></div>
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<style>.unitschema-1{
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background-image:url("/Structure/mmdb/mmdbimage.fcgi?uid=213628&type=2&unm=1");
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}</style><section class="graph-section" data-section="graph" id="biounit-section-1"></section>
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<section class="content_block" data-section="table"><table border="1" class="bucontent"><caption class="butbl_caption">Molecular Components in 7MXD<a class="help-img" href="/Structure/MMDB/docs/mmdb_help.html#MmdbsrvMolecularComponents" title="-click to see help"></a></caption>
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<thead><tr><th>Label</th>
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<th>Count</th>
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<th>Molecule</th>
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</tr></thead>
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<tbody data-bun="1" data-type="protein" id="unit1_protein_annotation"><tr><td class="butbl_inner_tbl_tit" colspan="3"><div style="float:left">Proteins (14 molecules)</div></td></tr>
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<tr data-row="0"><td class="molecule-label-cell"><div class="identical-molecules floatClear" id="chain-list-1-1"><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_A" id="mol-legend-1-1" class="protein-molecule-label-1" data-gi="2214225844" data-molid="1" style="color:#FFFFFF;background-color:#FF00FF" title="-Select icon for molecule information"><div class="protein-table-chain-label">A</div></a><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_F" id="mol-legend-1-4" class="protein-molecule-label-1" data-gi="2214225847" data-molid="4" style="color:#000000;background-color:#00FF99" title="-Select icon for molecule information"><div class="protein-table-chain-label">F</div></a><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_G" id="mol-legend-1-5" class="protein-molecule-label-1" data-gi="2214225848" data-molid="5" style="color:#000000;background-color:#CCCCCC" title="-Select icon for molecule information"><div class="protein-table-chain-label">G</div></a></div></td>
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<td>3</td>
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<td class="annotation-cell"><div class="graph-annot"><div class="molecule-name" title="Envelope Glycoprotein Gp120">Envelope Glycoprotein Gp120</div>
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<div class="annot-img-block" data-bun="1" data-gmolid="1" data-molids="1,4,5" id="molgraph-p-1-1"><img alt="Molecule annotation" src="/Structure/mmdb/images/bigLoader.gif"></div>
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</div></td>
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</tr>
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<tr data-row="1"><td class="molecule-label-cell"><div class="identical-molecules floatClear" id="chain-list-1-2"><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_C" id="mol-legend-1-2" class="protein-molecule-label-1" data-gi="2214225845" data-molid="2" style="color:#FFFFFF;background-color:#0000FF" title="-Select icon for molecule information"><div class="protein-table-chain-label">C</div></a><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_J" id="mol-legend-1-6" class="protein-molecule-label-1" data-gi="2214225849" data-molid="6" style="color:#000000;background-color:#FF9900" title="-Select icon for molecule information"><div class="protein-table-chain-label">J</div></a><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_S" id="mol-legend-1-8" class="protein-molecule-label-1" data-gi="2214225851" data-molid="8" style="color:#000000;background-color:#00FF00" title="-Select icon for molecule information"><div class="protein-table-chain-label">S</div></a></div></td>
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<td>3</td>
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<td class="annotation-cell"><div class="graph-annot"><div class="molecule-name" title="3bnc117 Antibody Heavy Chain">3bnc117 Antibody Heavy Chain</div>
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<div class="annot-img-block" data-bun="1" data-gmolid="2" data-molids="2,6,8" id="molgraph-p-1-2"><img alt="Molecule annotation" src="/Structure/mmdb/images/bigLoader.gif"></div>
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</div></td>
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</tr>
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<tr data-row="2"><td class="molecule-label-cell"><div class="identical-molecules floatClear" id="chain-list-1-3"><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_D" id="mol-legend-1-3" class="protein-molecule-label-1" data-gi="2214225846" data-molid="3" style="color:#FFFFFF;background-color:#996633" title="-Select icon for molecule information"><div class="protein-table-chain-label">D</div></a><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_K" id="mol-legend-1-7" class="protein-molecule-label-1" data-gi="2214225850" data-molid="7" style="color:#000000;background-color:#FF6666" title="-Select icon for molecule information"><div class="protein-table-chain-label">K</div></a><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_U" id="mol-legend-1-9" class="protein-molecule-label-1" data-gi="2214225852" data-molid="9" style="color:#000000;background-color:#00FFFF" title="-Select icon for molecule information"><div class="protein-table-chain-label">U</div></a></div></td>
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<td>3</td>
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<td class="annotation-cell"><div class="graph-annot"><div class="molecule-name" title="3bnc117 Antibody Light Chain">3bnc117 Antibody Light Chain</div>
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<div class="annot-img-block" data-bun="1" data-gmolid="3" data-molids="3,7,9" id="molgraph-p-1-3"><img alt="Molecule annotation" src="/Structure/mmdb/images/bigLoader.gif"></div>
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</div></td>
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</tr>
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<tr data-row="3"><td class="molecule-label-cell"><div class="identical-molecules floatClear" id="chain-list-1-4" style="text-align: center;"><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_X" id="mol-legend-1-10" class="protein-molecule-label-1" data-gi="2214225853" data-molid="10" style="color:#000000;background-color:#FFFF99" title="-Select icon for molecule information"><div class="protein-table-chain-label">X</div></a></div></td>
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<td>1</td>
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<td class="annotation-cell"><div class="graph-annot"><div class="molecule-name" title="J038 Antibody Heavy Chain">J038 Antibody Heavy Chain</div>
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<div class="annot-img-block" data-bun="1" data-gmolid="10" data-molids="10" id="molgraph-p-1-10"><img alt="Molecule annotation" src="/Structure/mmdb/images/bigLoader.gif"></div>
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</div></td>
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</tr>
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<tr data-row="4"><td class="molecule-label-cell"><div class="identical-molecules floatClear" id="chain-list-1-5" style="text-align: center;"><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_Y" id="mol-legend-1-11" class="protein-molecule-label-1" data-gi="2214225854" data-molid="11" style="color:#FFFFFF;background-color:#FF00FF" title="-Select icon for molecule information"><div class="protein-table-chain-label">Y</div></a></div></td>
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<td>1</td>
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<td class="annotation-cell"><div class="graph-annot"><div class="molecule-name" title="J038 Antibody Light Chain">J038 Antibody Light Chain</div>
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<div class="annot-img-block" data-bun="1" data-gmolid="11" data-molids="11" id="molgraph-p-1-11"><img alt="Molecule annotation" src="/Structure/mmdb/images/bigLoader.gif"></div>
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</div></td>
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</tr>
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<tr data-row="5"><td class="molecule-label-cell"><div class="identical-molecules floatClear" id="chain-list-1-6"><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_B" id="mol-legend-1-12" class="protein-molecule-label-1" data-gi="2214225855" data-molid="12" style="color:#FFFFFF;background-color:#0000FF" title="-Select icon for molecule information"><div class="protein-table-chain-label">B</div></a><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_I" id="mol-legend-1-13" class="protein-molecule-label-1" data-gi="2214225856" data-molid="13" style="color:#FFFFFF;background-color:#996633" title="-Select icon for molecule information"><div class="protein-table-chain-label">I</div></a><a href="//www.ncbi.nlm.nih.gov/protein/7MXD_H" id="mol-legend-1-14" class="protein-molecule-label-1" data-gi="2214225857" data-molid="14" style="color:#000000;background-color:#00FF99" title="-Select icon for molecule information"><div class="protein-table-chain-label">H</div></a></div></td>
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<td>3</td>
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<td class="annotation-cell"><div class="graph-annot"><div class="molecule-name" title="Envelope Glycoprotein Gp41">Envelope Glycoprotein Gp41</div>
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<div class="annot-img-block" data-bun="1" data-gmolid="12" data-molids="12,13,14" id="molgraph-p-1-12"><img alt="Molecule annotation" src="/Structure/mmdb/images/bigLoader.gif"></div>
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</div></td>
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</tr>
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</tbody>
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<tbody data-bun="1" data-type="chemical" id="unit1_chemical_annotation"><tr><td class="butbl_inner_tbl_tit" colspan="3"><div style="float:left">Chemicals and Non-standard biopolymers (146 molecules)</div></td></tr>
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<tr><td data-row="0"><div class="chem-label-box"><span class="chemical-molecule-label" id="mol-chem-legend-1-1" title="-No molecule information available"><a class="link chem_label" data-molids="15,16,17,18,19,20,21,22,29,30,36,37,38,39,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,63,64,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,91,92,93,94,99,100,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,129,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160" href="javascript:void(0)">1</a></span></div></td>
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<td><div class="chem-label">108</div></td>
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<td><div class="chem-name-thumb floatClear"><span class="chem-name" data-sid="900000000"><span class="mmdb-cham-name-nosid" title="2-acetamido-2-deoxy-beta-D-glucopyranose">2-acetamido-2-deoxy-beta-D-glucopyranose <span class="no-pubchem-available">(Link to PubChem not yet available)</span></span></span><span class="chem-image-holder" title="2-acetamido-2-deoxy-beta-D-glucopyranose"><img type="thumb" class="chemthumb" align="absmiddle" src="//pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=900000000" alt="2-acetamido-2-deoxy-beta-D-glucopyranose"></span></div></td>
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</tr>
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<tr><td data-row="1"><div class="chem-label-box"><span class="chemical-molecule-label" id="mol-chem-legend-1-2" title="-No molecule information available"><a class="link chem_label" data-molids="23,31,40,59,65,86,95,101" href="javascript:void(0)">2</a></span></div></td>
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<td><div class="chem-label">8</div></td>
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<td><div class="chem-name-thumb floatClear"><span class="chem-name" data-sid="900000000"><span class="mmdb-cham-name-nosid" title="beta-D-mannopyranose">beta-D-mannopyranose <span class="no-pubchem-available">(Link to PubChem not yet available)</span></span></span><span class="chem-image-holder" title="beta-D-mannopyranose"><img type="thumb" class="chemthumb" align="absmiddle" src="//pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=900000000" alt="beta-D-mannopyranose"></span></div></td>
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</tr>
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<tr><td data-row="2"><div class="chem-label-box"><span class="chemical-molecule-label" id="mol-chem-legend-1-3" title="-No molecule information available"><a class="link chem_label" data-molids="24,25,26,27,28,32,33,34,35,60,61,62,66,67,68,69,87,88,89,90,96,97,98,102,103,104,105" href="javascript:void(0)">3</a></span></div></td>
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<td><div class="chem-label">27</div></td>
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<td><div class="chem-name-thumb floatClear"><span class="chem-name" data-sid="900000000"><span class="mmdb-cham-name-nosid" title="alpha-D-mannopyranose">alpha-D-mannopyranose <span class="no-pubchem-available">(Link to PubChem not yet available)</span></span></span><span class="chem-image-holder" title="alpha-D-mannopyranose"><img type="thumb" class="chemthumb" align="absmiddle" src="//pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=900000000" alt="alpha-D-mannopyranose"></span></div></td>
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</tr>
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<tr><td data-row="3"><div class="chem-label-box"><span class="chemical-molecule-label" id="mol-chem-legend-1-4" title="-No molecule information available"><a class="link chem_label" data-molids="128,130,131" href="javascript:void(0)">4</a></span></div></td>
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<td><div class="chem-label">3</div></td>
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<td><div class="chem-name-thumb floatClear"><span class="chem-name" data-sid="900000000"><span class="mmdb-cham-name-nosid" title="PHOSPHATE ION">PHOSPHATE ION <span class="no-pubchem-available">(Link to PubChem not yet available)</span></span></span><span class="chem-image-holder" title="PHOSPHATE ION"><img type="thumb" class="chemthumb" align="absmiddle" src="//pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=900000000" alt="PHOSPHATE ION"></span></div></td>
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</table>
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<div style="margin:0.5em 1em;text-align:left; font-size:85%;">* Click molecule labels to explore molecular sequence information.<br/></div>
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</section>
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</div></div></div>
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</table>
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<div align="left" class="citing"><hr width="85%"/><div style="font-weight:bold">Citing MMDB</div><div class="citref" style="padding:0.2em;"><img style="border:0;text-align:left;height:15px;width:15px;margin-right:0.2em" src="//pubchem.ncbi.nlm.nih.gov/images/PubMed.gif"> <span style="color:#444"> Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. </span> <cite><a class="link" href="//www.ncbi.nlm.nih.gov/pubmed/24319143">"<span style="font-style:italic;"> MMDB and VAST+: tracking structural similarities between macromolecular complexes. <b style="font-size:90%">Nucleic Acids Res. 2014 Jan; 42(Database issue)</b>:D297-303</span></a></cite></div></div>
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