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5u5v

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Current revision (14:25, 6 March 2024) (edit) (undo)
 
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<StructureSection load='5u5v' size='340' side='right'caption='[[5u5v]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
<StructureSection load='5u5v' size='340' side='right'caption='[[5u5v]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5u5v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U5V FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5u5v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_RM11-1a Saccharomyces cerevisiae RM11-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U5V FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7WA:1H-BENZIMIDAZOL-4-AMINE'>7WA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.222&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5u5u|5u5u]], [[5u5w|5u5w]], [[5u5x|5u5x]], [[5u5y|5u5y]], [[5u5z|5u5z]], [[5u60|5u60]], [[5u61|5u61]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7WA:1H-BENZIMIDAZOL-4-AMINE'>7WA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SCRG_04081 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285006 Baker's yeast])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5u5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u5v OCA], [https://pdbe.org/5u5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u5v RCSB], [https://www.ebi.ac.uk/pdbsum/5u5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u5v ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5u5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u5v OCA], [http://pdbe.org/5u5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u5v RCSB], [http://www.ebi.ac.uk/pdbsum/5u5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u5v ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/B3LRE1_YEAS1 B3LRE1_YEAS1]
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Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled experiments at atomic resolution. To do so, we turned to a grid-based version of this method, GIST, readily implemented in molecular docking. Whereas the term only improves docking modestly in retrospective ligand enrichment, it could be added without disrupting performance. We thus turned to prospective docking of large libraries to investigate GIST's impact on ligand discovery, geometry, and water structure in a model cavity site well-suited to exploring these terms. Although top-ranked docked molecules with and without the GIST term often overlapped, many ligands were meaningfully prioritized or deprioritized; some of these were selected for testing. Experimentally, 13/14 molecules prioritized by GIST did bind, whereas none of the molecules that it deprioritized were observed to bind. Nine crystal complexes were determined. In six, the ligand geometry corresponded to that predicted by GIST, for one of these the pose without the GIST term was wrong, and three crystallographic poses differed from both predictions. Notably, in one structure, an ordered water molecule with a high GIST displacement penalty was observed to stay in place. Inclusion of this water-displacement term can substantially improve the hit rates and ligand geometries from docking screens, although the magnitude of its effects can be small and its impact in drug binding sites merits further controlled studies.
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Testing inhomogeneous solvation theory in structure-based ligand discovery.,Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK Proc Natl Acad Sci U S A. 2017 Aug 15;114(33):E6839-E6846. doi:, 10.1073/pnas.1703287114. Epub 2017 Jul 31. PMID:28760952<ref>PMID:28760952</ref>
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==See Also==
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*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5u5v" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Baker's yeast]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Fischer, M]]
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[[Category: Saccharomyces cerevisiae RM11-1a]]
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[[Category: Shoichet, B K]]
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[[Category: Fischer M]]
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[[Category: Cytochrome c peroxidase]]
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[[Category: Shoichet BK]]
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[[Category: Desolvation]]
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[[Category: Docking]]
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[[Category: Gist]]
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[[Category: Ligand binding]]
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[[Category: Model system]]
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[[Category: Oxidoreductase]]
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Current revision

CcP gateless cavity

PDB ID 5u5v

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