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==Cocktail experiment D: fragments 308 and 333 at 50mM concentration==
==Cocktail experiment D: fragments 308 and 333 at 50mM concentration==
<StructureSection load='5mb6' size='340' side='right' caption='[[5mb6]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
<StructureSection load='5mb6' size='340' side='right'caption='[[5mb6]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5mb6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MB6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5mb6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MB6 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.201&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3t7p|3t7p]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </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=5mb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mb6 OCA], [https://pdbe.org/5mb6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mb6 RCSB], [https://www.ebi.ac.uk/pdbsum/5mb6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mb6 ProSAT]</span></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=5mb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mb6 OCA], [http://pdbe.org/5mb6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mb6 RCSB], [http://www.ebi.ac.uk/pdbsum/5mb6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mb6 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA]
Successful optimization of a given lead scaffold requires thorough binding-site mapping of the target protein particular in regions remote from the catalytic center where high conservation across protein families is given. We screened a 361-entry fragment library for binding to the aspartic protease endothiapepsin by crystallography. This enzyme is frequently used as a surrogate for the design of renin and beta-secretase inhibitors. A hit rate of 20% was achieved, providing 71 crystal structures. Here, we discuss 45 binding poses of fragments accommodated in pockets remote from the catalytic dyad. Three major hot spots are discovered in remote binding areas: Asp81, Asp119, and Phe291. Compared to the dyad binders, bulkier fragments occupy these regions. Many of the discovered fragments suggest an optimization concept on how to grow them into larger ligands occupying adjacent binding pockets that will possibly endow them with the desired selectivity for one given member of a protein family.


Experimental Active-Site Mapping by Fragments: Hot Spots Remote from the Catalytic Center of Endothiapepsin.,Radeva N, Krimmer SG, Stieler M, Fu K, Wang X, Ehrmann FR, Metz A, Huschmann FU, Weiss MS, Mueller U, Schiebel J, Heine A, Klebe G J Med Chem. 2016 Aug 25;59(16):7561-75. doi: 10.1021/acs.jmedchem.6b00645. Epub, 2016 Aug 12. PMID:27463859<ref>PMID:27463859</ref>
==See Also==
 
*[[Pepsin|Pepsin]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5mb6" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Cryphonectria parasitica]]
[[Category: Cryphonectria parasitica]]
[[Category: Endothiapepsin]]
[[Category: Large Structures]]
[[Category: Heine, A]]
[[Category: Heine A]]
[[Category: Klebe, G]]
[[Category: Klebe G]]
[[Category: Koester, H]]
[[Category: Koester H]]
[[Category: Radeva, N]]
[[Category: Radeva N]]
[[Category: Cocktail experiment]]
[[Category: Hydrolase]]

Latest revision as of 21:36, 1 November 2023

Cocktail experiment D: fragments 308 and 333 at 50mM concentrationCocktail experiment D: fragments 308 and 333 at 50mM concentration

Structural highlights

5mb6 is a 1 chain structure with sequence from Cryphonectria parasitica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.201Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CARP_CRYPA

See Also

5mb6, resolution 1.20Å

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