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173 lines
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<title>8TO9: Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP</title>
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<meta name="description" content="Envelope glycoprotein gp120Envelope glycoprotein gp41TRNM-f*01 heavy chainTRNM-f*01 light chain2-acetamido-2-deoxy-beta-D-glucopyranosebeta-D-mannopyranose">
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<meta name="keywords" content="Envelope glycoprotein gp120, Envelope glycoprotein gp41, TRNM-f*01 heavy chain, TRNM-f*01 light chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, 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="8TO9 - 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="250724" data-pdbid="8TO9" id="structure-title"><a class="link title-pdbid" href="http://www.rcsb.org/pdb/explore/explore.do?structureId=8TO9" style="font-weight:600;margin:0;">8TO9: </a><span>Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP</span></h1>
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<div class="floatClear" id="infor-detail"><div class="reference_section" data-pmids="39471811" 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="250724"/></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=8TO9" title="PDB ID">8TO9</a><a id="download-pdb-file" class="__button" tabindex="-1" href="https://files.rcsb.org/download/8TO9.pdb" title="Download PDB file" download="8TO9.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><td class="H4 property-name">MMDB ID: </td>
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<td style="font-weight:bold"><span class="info-item">250724</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;">2023/8/3<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">2024/12</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>4.03 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="Homo sapiens">Homo sapiens</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>
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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>A, B, C, I, J, Z</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>D, E, F, G, H, L</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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</section>
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<!-- end of StructureInfo -->
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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 8TO9: dodecameric; 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=250724&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 8TO9<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 (12 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/8TO9_A" id="mol-legend-1-1" class="protein-molecule-label-1" data-gi="2784091189" 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/8TO9_B" id="mol-legend-1-2" class="protein-molecule-label-1" data-gi="2784091190" data-molid="2" 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/8TO9_C" id="mol-legend-1-3" class="protein-molecule-label-1" data-gi="2784091191" data-molid="3" style="color:#FFFFFF;background-color:#996633" title="-Select icon for molecule information"><div class="protein-table-chain-label">C</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="1,2,3" 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/8TO9_D" id="mol-legend-1-4" class="protein-molecule-label-1" data-gi="2784091192" data-molid="4" style="color:#000000;background-color:#00FF99" title="-Select icon for molecule information"><div class="protein-table-chain-label">D</div></a><a href="//www.ncbi.nlm.nih.gov/protein/8TO9_E" id="mol-legend-1-5" class="protein-molecule-label-1" data-gi="2784091193" data-molid="5" style="color:#000000;background-color:#CCCCCC" title="-Select icon for molecule information"><div class="protein-table-chain-label">E</div></a><a href="//www.ncbi.nlm.nih.gov/protein/8TO9_H" id="mol-legend-1-8" class="protein-molecule-label-1" data-gi="2784091196" data-molid="8" style="color:#000000;background-color:#00FF00" 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="Trnm-f*01 Heavy Chain">Trnm-f*01 Heavy Chain</div>
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<div class="annot-img-block" data-bun="1" data-gmolid="4" data-molids="4,5,8" id="molgraph-p-1-4"><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/8TO9_F" id="mol-legend-1-6" class="protein-molecule-label-1" data-gi="2784091194" data-molid="6" style="color:#000000;background-color:#FF9900" title="-Select icon for molecule information"><div class="protein-table-chain-label">F</div></a><a href="//www.ncbi.nlm.nih.gov/protein/8TO9_G" id="mol-legend-1-7" class="protein-molecule-label-1" data-gi="2784091195" data-molid="7" style="color:#000000;background-color:#FF6666" title="-Select icon for molecule information"><div class="protein-table-chain-label">G</div></a><a href="//www.ncbi.nlm.nih.gov/protein/8TO9_L" id="mol-legend-1-11" class="protein-molecule-label-1" data-gi="2784091199" data-molid="11" style="color:#FFFFFF;background-color:#FF00FF" title="-Select icon for molecule information"><div class="protein-table-chain-label">L</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="Trnm-f*01 Light Chain">Trnm-f*01 Light Chain</div>
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<div class="annot-img-block" data-bun="1" data-gmolid="6" data-molids="6,7,11" id="molgraph-p-1-6"><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"><a href="//www.ncbi.nlm.nih.gov/protein/8TO9_I" id="mol-legend-1-9" class="protein-molecule-label-1" data-gi="2784091197" data-molid="9" style="color:#000000;background-color:#00FFFF" title="-Select icon for molecule information"><div class="protein-table-chain-label">I</div></a><a href="//www.ncbi.nlm.nih.gov/protein/8TO9_J" id="mol-legend-1-10" class="protein-molecule-label-1" data-gi="2784091198" data-molid="10" style="color:#000000;background-color:#FFFF99" title="-Select icon for molecule information"><div class="protein-table-chain-label">J</div></a><a href="//www.ncbi.nlm.nih.gov/protein/8TO9_Z" id="mol-legend-1-12" class="protein-molecule-label-1" data-gi="2784091200" data-molid="12" style="color:#FFFFFF;background-color:#0000FF" title="-Select icon for molecule information"><div class="protein-table-chain-label">Z</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="9" data-molids="9,10,12" id="molgraph-p-1-9"><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 (82 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="-Select icon for PubChem compound information"><a class="link chem_label" data-molids="13,14,15,16,18,19,20,21,22,23,24,25,26,27,28,29,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94" href="//pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=497625855">1</a></span></div></td>
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<td><div class="chem-label">78</div></td>
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<td><div class="chem-name-thumb floatClear"><span class="chem-name" data-sid="497625855"><a class="link mmdb-chem-name" href="//pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=497625855" title="2-acetamido-2-deoxy-beta-D-glucopyranose">2-acetamido-2-deoxy-beta-D-glucopyranose</a></span><span class="chem-image-holder" title="2-acetamido-2-deoxy-beta-D-glucopyranose"><a href="//pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=497625855"><img type="thumb" class="chemthumb" align="absmiddle" src="//pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=497625855" alt="2-acetamido-2-deoxy-beta-D-glucopyranose"></a></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="-Select icon for PubChem compound information"><a class="link chem_label" data-molids="17,30,43,50" href="//pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=497625857">2</a></span></div></td>
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<td><div class="chem-label">4</div></td>
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<td><div class="chem-name-thumb floatClear"><span class="chem-name" data-sid="497625857"><a class="link mmdb-chem-name" href="//pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=497625857" title="beta-D-mannopyranose">beta-D-mannopyranose</a></span><span class="chem-image-holder" title="beta-D-mannopyranose"><a href="//pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=497625857"><img type="thumb" class="chemthumb" align="absmiddle" src="//pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=497625857" alt="beta-D-mannopyranose"></a></span></div></td>
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</tr>
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</tbody>
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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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<!-- end annotations -->
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</td></tr>
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</table>
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<!-- Start of citation -->
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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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