5u5y: Difference between revisions

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==CcP gateless cavity==
==CcP gateless cavity==
<StructureSection load='5u5y' size='340' side='right' caption='[[5u5y]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
<StructureSection load='5u5y' size='340' side='right'caption='[[5u5y]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5u5y]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U5Y FirstGlance]. <br>
<table><tr><td colspan='2'>[[5u5y]] 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=5U5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U5Y FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7W4:2-METHYLIMIDAZO[1,2-A]PYRIDIN-3-AMINE'>7W4</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5u5u|5u5u]], [[5u5v|5u5v]], [[5u5w|5u5w]], [[5u5x|5u5x]], [[5u5z|5u5z]], [[5u60|5u60]], [[5u61|5u61]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7W4:2-METHYLIMIDAZO[1,2-A]PYRIDIN-3-AMINE'>7W4</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
<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=5u5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u5y OCA], [http://pdbe.org/5u5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u5y RCSB], [http://www.ebi.ac.uk/pdbsum/5u5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u5y ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5u5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u5y OCA], [https://pdbe.org/5u5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u5y RCSB], [https://www.ebi.ac.uk/pdbsum/5u5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u5y ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/B3LRE1_YEAS1 B3LRE1_YEAS1]
Proteins fluctuate between alternative conformations, which presents a challenge for ligand discovery because such flexibility is difficult to treat computationally owing to problems with conformational sampling and energy weighting. Here we describe a flexible docking method that samples and weights protein conformations using experimentally derived conformations as a guide. The crystallographically refined occupancies of these conformations, which are observable in an apo receptor structure, define energy penalties for docking. In a large prospective library screen, we identified new ligands that target specific receptor conformations of a cavity in cytochrome c peroxidase, and we confirm both ligand pose and associated receptor conformation predictions by crystallography. The inclusion of receptor flexibility led to ligands with new chemotypes and physical properties. By exploiting experimental measures of loop and side-chain flexibility, this method can be extended to the discovery of new ligands for hundreds of targets in the Protein Data Bank for which similar experimental information is available.


Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.,Fischer M, Coleman RG, Fraser JS, Shoichet BK Nat Chem. 2014 Jul;6(7):575-83. doi: 10.1038/nchem.1954. Epub 2014 May 25. PMID:24950326<ref>PMID:24950326</ref>
==See Also==
 
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5u5y" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Fischer, M]]
[[Category: Large Structures]]
[[Category: Shoichet, B K]]
[[Category: Saccharomyces cerevisiae RM11-1a]]
[[Category: Cytochrome c peroxidase]]
[[Category: Fischer M]]
[[Category: Desolvation]]
[[Category: Shoichet BK]]
[[Category: Docking]]
[[Category: Gist]]
[[Category: Ligand binding]]
[[Category: Model system]]
[[Category: Oxidoreductase]]
[[Category: Water]]

Latest revision as of 17:25, 6 March 2024

CcP gateless cavityCcP gateless cavity

Structural highlights

5u5y is a 1 chain structure with sequence from Saccharomyces cerevisiae RM11-1a. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B3LRE1_YEAS1

See Also

5u5y, resolution 1.30Å

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