View source for 4nvm


==Predicting protein conformational response in prospective ligand discovery==
<StructureSection load='4nvm' size='340' side='right'caption='[[4nvm]], [[Resolution|resolution]] 1.51&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4nvm]] 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=4NVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NVM FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.51&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2O0:3-(1H-BENZIMIDAZOL-1-YL)PROPANAMIDE'>2O0</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=4nvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nvm OCA], [https://pdbe.org/4nvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nvm RCSB], [https://www.ebi.ac.uk/pdbsum/4nvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nvm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/B3LRE1_YEAS1 B3LRE1_YEAS1] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4nvm" style="background-color:#fffaf0;"></div>

==See Also==
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae RM11-1a]]
[[Category: Fischer M]]
[[Category: Fraser JS]]