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<a href="/I-TASSER">●<span>I-TASSER</span></a>
<a href="/I-TASSER-MTD">●<span>I-TASSER-MTD</span></a>
<a href="/C-I-TASSER">●<span>C-I-TASSER</span></a>
<a href="/CR-I-TASSER">●<span>CR-I-TASSER</span></a>
<a href="/QUARK">●<span>QUARK</span></a>
<a href="/C-QUARK">●<span>C-QUARK</span></a>
<a href="/LOMETS">●<span>LOMETS</span></a>
<a href="/MUSTER">●<span>MUSTER</span></a>
<a href="/CEthreader">●<span>CEthreader</span></a>
<a href="/SEGMER">●<span>SEGMER</span></a>
<a href="/DeepFold">●<span>DeepFold</span></a>
<a href="/DeepFoldRNA">●<span>DeepFoldRNA</span></a>
<a href="/FoldDesign">●<span>FoldDesign</span></a>
<a href="/COFACTOR">●<span>COFACTOR</span></a>
<a href="/COACH">●<span>COACH</span></a>
<a href="/MetaGO">●<span>MetaGO</span></a>
<a href="/TripletGO">●<span>TripletGO</span></a>
<a href="/IonCom">●<span>IonCom</span></a>
<a href="/FG-MD">●<span>FG-MD</span></a>
<a href="/ModRefiner">●<span>ModRefiner</span></a>
<a href="/REMO">●<span>REMO</span></a>
<a href="/DEMO">●<span>DEMO</span></a>
<a href="/DEMO-EM">●<span>DEMO-EM</span></a>
<a href="/spring">●<span>SPRING</span></a>
<a href="/COTH">●<span>COTH</span></a>
<a href="/Threpp">●<span>Threpp</span></a>
<a href="/PEPPI">●<span>PEPPI</span></a>
<a href="/BSpred">●<span>BSpred</span></a>
<a href="/ANGLOR">●<span>ANGLOR</span></a>
<a href="/EDock">●<span>EDock</span></a>
<a href="/BSP-SLIM">●<span>BSP-SLIM</span></a>
<a href="/SAXSTER">●<span>SAXSTER</span></a>
<a href="/FUpred">●<span>FUpred</span></a>
<a href="/ThreaDom">●<span>ThreaDom</span></a>
<a href="/ThreaDomEx">●<span>ThreaDomEx</span></a>
<a href="/EvoDesign">●<span>EvoDesign</span></a>
<a href="/BindProf">●<span>BindProf</span></a>
<a href="/BindProfX">●<span>BindProfX</span></a>
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<a href="/ResQ">●<span>ResQ</span></a>
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<a href="/TM-score">●<span>TM-score</span></a>
<a href="/TM-align">●<span>TM-align</span></a>
<a href="/US-align">●<span>US-align</span></a>
<a href="/MM-align">●<span>MM-align</span></a>
<a href="/RNA-align">●<span>RNA-align</span></a>
<a href="/NW-align">●<span>NW-align</span></a>
<a href="/LS-align">●<span>LS-align</span></a>
<a href="/EDTSurf">●<span>EDTSurf</span></a>
<a href="/MVP">●<span>MVP</span></a>
<a href="/MVP-Fit">●<span>MVP-Fit</span></a>
<a href="/SPICKER">●<span>SPICKER</span></a>
<a href="/HAAD">●<span>HAAD</span></a>
<a href="/PSSpred">●<span>PSSpred</span></a>
<a href="/3DRobot">●<span>3DRobot</span></a>
<a href="/MR-REX">●<span>MR-REX</span></a>
<a href="/I-TASSER-MR">●<span>I-TASSER-MR</span></a>
<a href="/SVMSEQ">●<span>SVMSEQ</span></a>
<a href="/NeBcon">●<span>NeBcon</span></a>
<a href="/ResPRE">●<span>ResPRE</span></a>
<a href="/TripletRes">●<span>TripletRes</span></a>
<a href="/DeepPotential">●<span>DeepPotential</span></a>
<a href="/WDL-RF">●<span>WDL-RF</span></a>
<a href="/ATPbind">●<span>ATPbind</span></a>
<a href="/DockRMSD">●<span>DockRMSD</span></a>
<a href="/DeepMSA">●<span>DeepMSA</span></a>
<a href="/FASPR">●<span>FASPR</span></a>
<a href="/EM-Refiner">●<span>EM-Refiner</span></a>
<a href="/GPU-I-TASSER">●<span>GPU-I-TASSER</span></a>
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<a href="/BioLiP">●<span>BioLiP</span></a>
<a href="/Ecoli">●<span>E. coli</span></a>
<a href="/GLASS">●<span>GLASS</span></a>
<a href="/GPCR-HGmod">●<span>GPCR-HGmod</span></a>
<a href="/GPCR-RD">●<span>GPCR-RD</span></a>
<a href="/GPCR-EXP">●<span>GPCR-EXP</span></a>
<a href="/Tara-3D">●<span>Tara-3D</span></a>
<a href="/TM-fold">●<span>TM-fold</span></a>
<a href="/decoys">●<span>DECOYS</span></a>
<a href="/potential">●<span>POTENTIAL</span></a>
<a href="/RW">●<span>RW/RWplus</span></a>
<a href="/EvoEF">●<span>EvoEF</span></a>
<a href="/HPSF">●<span>HPSF</span></a>
<a href="/THE-DB">●<span>THE-DB</span></a>
<a href="/ADDRESS">●<span>ADDRESS</span></a>
<a href="/Alpaca-Antibody">●<span>Alpaca-Antibody</span></a>
<a href="/casp7">●<span>CASP7</span></a>
<a href="/casp8">●<span>CASP8</span></a>
<a href="/casp9">●<span>CASP9</span></a>
<a href="/casp10">●<span>CASP10</span></a>
<a href="/casp11">●<span>CASP11</span></a>
<a href="/casp12">●<span>CASP12</span></a>
<a href="/casp13">●<span>CASP13</span></a>
<a href="/casp14">●<span>CASP14</span></a>
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<tr><td><h1 align=center>Structure of PDB 5lyb Chain q0 Binding Site BS02</h1></td></tr>
<tr><td>
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<div id="titleText">Receptor Information</div>
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<tr><td>>5lyb Chain q0 (length=52) Species: <a href="https://ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4932" target=_blank>4932</a> (Saccharomyces cerevisiae)
[<a href=ssearch.cgi?seq_type=protein&sequence=IIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQLRPKKKLK target=_blank>Search protein sequence</a>]
[<a href=output/5lybq0.pdb.gz>Download receptor structure</a>]
[<a href=?pdbid=5lyb&chain=q0&outfmt=1 download=5lybq0.pdb>Download structure with residue number starting from 1</a>]
[<a href=?pdb=5lyb&chain=q0 target=_blank>View receptor structure</a>]
</td></tr>
<tr><td><span title="Only residues with experimentally determined coordinates are included. Residues unobserved in the structure are excluded.">IIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQLRPKKK<br>LK</span></td></tr>
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<div id="titleText">Ligand information</div>
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<a href=https://cdn.rcsb.org/images/ccd/labeled/M/MG.svg target=_blank><img src=https://cdn.rcsb.org/images/ccd/labeled/M/MG.svg width=400></a>
</td>
<td>
<table>
<tr BGCOLOR="#DEDEDE"><td align=center><a href=https://wwpdb.org/data/ccd target=_blank>Ligand ID</a></td><td><span title="The ligand ID follows the
Chemical Component Dictionary (CCD)
used by the PDB database."><a href=https://rcsb.org/ligand/MG>MG</a></span></td></tr>
<tr><td align=center><a href=https://inchi-trust.org target=_blank>InChI</a></td><td>InChI=1S/Mg/q+2</td></tr>
<tr BGCOLOR="#DEDEDE"><td align=center><a href=https://inchi-trust.org target=_blank>InChIKey</a></td><td>JLVVSXFLKOJNIY-UHFFFAOYSA-N</td></tr>
<tr><td align=center>SMILES</td><td><table width=100%><tr BGCOLOR='#DEDEDE'><th>Software</th><th>SMILES</th></tr><tr><td>ACDLabs 10.04<br>OpenEye OEToolkits 1.5.0</td><td>[Mg+2]</td></tr><tr><td>CACTVS 3.341</td><td>[Mg++]</td></tr></table></td></tr>
<tr BGCOLOR="#DEDEDE"><td align=center>Formula</td><td>Mg</td></tr>
<tr><td align=center>Name</td><td>MAGNESIUM ION</td></tr>
<tr BGCOLOR="#DEDEDE"><td align=center><a href=https://www.ebi.ac.uk/chembl target=_blank>ChEMBL</a></td><td><a href="https://www.ebi.ac.uk/chembl/compound_report_card/" target=_blank></a></td></tr>
<tr><td align=center><a href=https://go.drugbank.com target=_blank>DrugBank</a></td><td><a href="https://go.drugbank.com/drugs/DB01378" target=_blank>DB01378</a></td></tr>
<tr BGCOLOR="#DEDEDE"><td align=center><a href=https://zinc.docking.org>ZINC</a></td><td><a href="https://zinc.docking.org/substances/
" target=_blank>
</a></td></tr>
<tr><td align=center>PDB chain</td><td>5lyb Chain 5 Residue 4057
[<a href=output/5lyb_MG_5_11.pdb.gz>Download ligand structure</a>]
[<a href=?pdb=5lyb&chain=5&lig3=MG&ligIdx=11&outfmt=1 download=5lyb_MG_5_11.pdb>Download structure with residue number starting from 1</a>]
[<a href=?pdb=5lyb&chain=5&lig3=MG&ligIdx=11 target=_blank>View ligand structure</a>]
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<th>Global view</th><th>Local view</th><th>Structure summary</th>
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<tr><td align=center><strong>PDB</strong><td><span title="Search BioLiP entries from the same structure"><a href=qsearch.cgi?pdbid=5lyb target=_blank>5lyb</a></span> ?</td></tr>
<tr BGCOLOR="#DEDEDE"><td align=center><strong>Resolution</strong><td>3.25 Å</td></tr>
<tr><td align=center><strong>Binding residue<br>(original residue number in PDB)</strong><td>R102 R111</td></tr>
<tr BGCOLOR="#DEDEDE"><td align=center><strong>Binding residue<br>(residue number reindexed from 1)</strong><td>R26 R35</td></tr>
<tr><td align=center><strong><span title="
Each protein-ligand interaction is assigned an annotation score ranging from
1 to 5. Higher score suggests greater biological relevance.
If the UniProt protein corresponding to the receptor chain is mapped to at
least one Rhea reaction, all non-water substrates and products of the
reaction(s) are converted to 1024 bit Morgan fingerprint (ECFP4). Their
chemical similarity to the ligand in question can then be measured by
Tanimoto Coefficient (TC). The highest TC among all substrates/products to
the ligand is used to assign the annotation score: TC of [0,0.4), [0.4,0.6),
[0.6,0.8), [0.8,1) and 1 correspond to annotation score of 1, 2, 3, 4 and 5, respectively.
If the receptor protein cannot be mapped to Rhea, the annotation score is
assigned based on FireDB classification of ligands, where cognate, ambiguous
and non-cognate ligands are assigned score of 1, 3, and 4, respectively.
">Annotation score</span></strong><td><span title=FireDB:cognate>4 <img src=images/4-star.svg width=75></span></td></tr>
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<div id="titleText">Enzymatic activity</div>
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<td width=10%><strong>Enzyme Commision number</strong></td>
<td width=90% align=left><a href=https://enzyme.expasy.org/EC/? target=_blank>?</a></td>
</tr>
</table>
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<div id="titleText">Gene Ontology</div>
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<tr BGCOLOR="#DEDEDE" align=center>
<th width=10% align=right><strong></strong></th>
<th width=90% align=left><span title="View Molecular Function annotation for UniProt protein P0CH08"><strong><a href="https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=P0CH08&aspect=molecular_function" target=_blank>Molecular Function</a></strong></a></th>
</tr>
<tr BGCOLOR="#F2F2F2">
<td align=center width=10%><a href="https://ebi.ac.uk/QuickGO/term/GO:0003735" target=_blank>GO:0003735</td>
<td align=left width=90%>structural constituent of ribosome</td>
</tr>
</table>
</tr>
<tr>
<table width=100%>
<tr BGCOLOR="#DEDEDE" align=center>
<th width=10% align=right><strong></strong></th>
<th width=90% align=left><span title="View Biological Process annotation for UniProt protein P0CH08"><strong><a href="https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=P0CH08&aspect=biological_process" target=_blank>Biological Process</a></strong></a></th>
</tr>
<tr BGCOLOR="#F2F2F2">
<td align=center width=10%><a href="https://ebi.ac.uk/QuickGO/term/GO:0006412" target=_blank>GO:0006412</td>
<td align=left width=90%>translation</td>
</tr>
</table>
</tr>
<tr>
<table width=100%>
<tr BGCOLOR="#DEDEDE" align=center>
<th width=10% align=right><strong></strong></th>
<th width=90% align=left><span title="View Cellular Component annotation for UniProt protein P0CH08"><strong><a href="https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=P0CH08&aspect=cellular_component" target=_blank>Cellular Component</a></strong></a></th>
</tr>
<tr BGCOLOR="#F2F2F2">
<td align=center width=10%><a href="https://ebi.ac.uk/QuickGO/term/GO:0005840" target=_blank>GO:0005840</td>
<td align=left width=90%>ribosome</td>
</tr>
</table>
</tr>
</table>
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<tr valign=bottom>
<td align=center width=28%><span title="View graph for Molecular Function.
Grey and white boxes indidate GO terms directly annotated to the protein by SIFTS and their parent terms, respectively."><a href=output/5lyb_q0_F.svg target=_blank><img src=output/5lyb_q0_F.svg style="display:block;" width="100%"><br>View graph for<br>Molecular Function</a></td>
<td align=center width=43%><span title="View graph for Biological Process.
Grey and white boxes indidate GO terms directly annotated to the protein by SIFTS and their parent terms, respectively."><a href=output/5lyb_q0_P.svg target=_blank><img src=output/5lyb_q0_P.svg style="display:block;" width="100%"><br>View graph for<br>Biological Process</a></td>
<td align=center width=27%><span title="View graph for Cellular Component.
Grey and white boxes indidate GO terms directly annotated to the protein by SIFTS and their parent terms, respectively."><a href=output/5lyb_q0_C.svg target=_blank><img src=output/5lyb_q0_C.svg style="display:block;" width="100%"><br>View graph for<br>Cellular Component</a></td>
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<div id="titleText">External links</div>
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<tr><td align=center width=10%><strong>PDB</strong></td>
<td width=90%><a href=https://rcsb.org/structure/5lyb target=_blank>RCSB:5lyb</a>,
<a href=https://ebi.ac.uk/pdbe/entry/pdb/5lyb target=_blank>PDBe:5lyb</a>,
<a href=https://pdbj.org/mine/summary/5lyb target=_blank>PDBj:5lyb</a></td> </tr>
<tr BGCOLOR="#DEDEDE"> <td align=center><strong>PDBsum</strong></td><td><a href=http://ebi.ac.uk/pdbsum/5lyb target=_blank>5lyb</a></td></tr>
<tr> <td align=center><strong>PubMed</strong></td><td><a href=https://pubmed.ncbi.nlm.nih.gov/27827794
target=_blank>27827794
</a></td></tr>
<tr BGCOLOR="#DEDEDE"><td align=center><strong>UniProt</strong></td><td><a href=https://uniprot.org/uniprot/P0CH08 target=_blank>P0CH08</a>|RL40A_YEAST Ubiquitin-ribosomal protein eL40A fusion protein (Gene Name=RPL40A)</tr>
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