4jmz - Revision history

OCA at 12:05, 1 March 2024

OCA — Fri, 01 Mar 2024 12:05:16 GMT

←Older revision		Revision as of 12:05, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4jmz]] 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=4JMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JMZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jmz]] 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=4JMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JMZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1M2:N-METHYL-1H-BENZIMIDAZOL-2-AMINE'>1M2</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]] 1.82Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1M2:N-METHYL-1H-BENZIMIDAZOL-2-AMINE'>1M2</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'>[https://proteopedia.org/fgij/fg.htm?mol=4jmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jmz OCA], [https://pdbe.org/4jmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jmz RCSB], [https://www.ebi.ac.uk/pdbsum/4jmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jmz 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=4jmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jmz OCA], [https://pdbe.org/4jmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jmz RCSB], [https://www.ebi.ac.uk/pdbsum/4jmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jmz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/B3LRE1_YEAS1 B3LRE1_YEAS1]		[https://www.uniprot.org/uniprot/B3LRE1_YEAS1 B3LRE1_YEAS1]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A key challenge in structure-based discovery is accounting for modulation of protein-ligand interactions by ordered and bulk solvent. To investigate this, we compared ligand binding to a buried cavity in Cytochrome c Peroxidase (CcP), where affinity is dominated by a single ionic interaction, versus a cavity variant partly opened to solvent by loop deletion. This opening had unexpected effects on ligand orientation, affinity, and ordered water structure. Some ligands lost over ten-fold in affinity and reoriented in the cavity, while others retained their geometries, formed new interactions with water networks, and improved affinity. To test our ability to discover new ligands against this opened site prospectively, a 534,000 fragment library was docked against the open cavity using two models of ligand solvation. Using an older solvation model that prioritized many neutral molecules, three such uncharged docking hits were tested, none of which was observed to bind; these molecules were not highly ranked by the new, context-dependent solvation score. Using this new method, another 15 highly-ranked molecules were tested for binding. In contrast to the previous result, 14 of these bound detectably, with affinities ranging from 8 microM to 2 mM. In crystal structures, four of these new ligands superposed well with the docking predictions but two did not, reflecting unanticipated interactions with newly ordered waters molecules. Comparing recognition between this open cavity and its buried analog begins to isolate the roles of ordered solvent in a system that lends itself readily to prospective testing and that may be broadly useful to the community.
-
-	Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities.,Barelier S, Boyce SE, Fish I, Fischer M, Goodin DB, Shoichet BK PLoS One. 2013 Jul 18;8(7):e69153. doi: 10.1371/journal.pone.0069153. Print 2013. PMID:23874896<ref>PMID:23874896</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4jmz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]		*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:24, 24 November 2022

OCA — Thu, 24 Nov 2022 11:24:24 GMT

←Older revision		Revision as of 11:24, 24 November 2022
Line 1:		Line 1:

	==Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine==		==Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine==
-	<StructureSection load='4jmz' size='340' side='right' caption='[[4jmz]], [[Resolution\|resolution]] 1.82Å' scene=''>	+	<StructureSection load='4jmz' size='340' side='right'caption='[[4jmz]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jmz]] 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=4JMZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jmz]] 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=4JMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JMZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1M2:N-METHYL-1H-BENZIMIDAZOL-2-AMINE'>1M2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1M2:N-METHYL-1H-BENZIMIDAZOL-2-AMINE'>1M2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kxn\|1kxn]], [[1kxm\|1kxm]], [[4jm5\|4jm5]], [[4jm6\|4jm6]], [[4jm8\|4jm8]], [[4jm9\|4jm9]], [[4jma\|4jma]], [[4jmw\|4jmw]], [[4jpl\|4jpl]], [[4jpt\|4jpt]], [[4jpu\|4jpu]], [[4jqj\|4jqj]], [[4jqk\|4jqk]], [[4jqm\|4jqm]], [[4jqn\|4jqn]], [[4jmb\|4jmb]], [[4jms\|4jms]], [[4jmt\|4jmt]], [[4jmv\|4jmv]], [[4jn0\|4jn0]]</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=4jmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jmz OCA], [https://pdbe.org/4jmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jmz RCSB], [https://www.ebi.ac.uk/pdbsum/4jmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jmz ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP1 CCP CPO YKR066C, SCRG_04081 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285006 Baker's yeast])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=4jmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jmz OCA], [~~http~~://pdbe.org/4jmz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jmz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jmz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jmz ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B3LRE1_YEAS1 B3LRE1_YEAS1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]	+	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baker's yeast~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Cytochrome~~-~~c peroxidase~~]]	+	[[Category: Saccharomyces cerevisiae RM11-1a]]
-	[[Category: Barelier, S]]	+	[[Category: Barelier S]]
-	[[Category: Fischer, M]]	+	[[Category: Fischer M]]
-	~~[[Category: Bulk solvent]]~~	+
-	~~[[Category: Docking]]~~	+
-	~~[[Category: Ligand binding]]~~	+
-	~~[[Category: Model system]]~~	+
-	~~[[Category: Ordered water]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 13:11, 11 August 2016

OCA — Thu, 11 Aug 2016 13:11:29 GMT

←Older revision		Revision as of 13:11, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine==		==Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine==
	<StructureSection load='4jmz' size='340' side='right' caption='[[4jmz]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='4jmz' size='340' side='right' caption='[[4jmz]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jmz]] is a 1 chain structure with sequence from [http://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=4JMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jmz]] 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=4JMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JMZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1M2:N-METHYL-1H-BENZIMIDAZOL-2-AMINE'>1M2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1M2:N-METHYL-1H-BENZIMIDAZOL-2-AMINE'>1M2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kxn\|1kxn]], [[1kxm\|1kxm]], [[4jm5\|4jm5]], [[4jm6\|4jm6]], [[4jm8\|4jm8]], [[4jm9\|4jm9]], [[4jma\|4jma]], [[4jmw\|4jmw]], [[4jpl\|4jpl]], [[4jpt\|4jpt]], [[4jpu\|4jpu]], [[4jqj\|4jqj]], [[4jqk\|4jqk]], [[4jqm\|4jqm]], [[4jqn\|4jqn]], [[4jmb\|4jmb]], [[4jms\|4jms]], [[4jmt\|4jmt]], [[4jmv\|4jmv]], [[4jn0\|4jn0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kxn\|1kxn]], [[1kxm\|1kxm]], [[4jm5\|4jm5]], [[4jm6\|4jm6]], [[4jm8\|4jm8]], [[4jm9\|4jm9]], [[4jma\|4jma]], [[4jmw\|4jmw]], [[4jpl\|4jpl]], [[4jpt\|4jpt]], [[4jpu\|4jpu]], [[4jqj\|4jqj]], [[4jqk\|4jqk]], [[4jqm\|4jqm]], [[4jqn\|4jqn]], [[4jmb\|4jmb]], [[4jms\|4jms]], [[4jmt\|4jmt]], [[4jmv\|4jmv]], [[4jn0\|4jn0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP1 CCP CPO YKR066C, SCRG_04081 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285006 ~~Saccharomyces cerevisiae RM11-1a~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP1 CCP CPO YKR066C, SCRG_04081 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285006 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=4jmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jmz RCSB], [http://www.ebi.ac.uk/pdbsum/4jmz PDBsum]</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=4jmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jmz OCA], [http://pdbe.org/4jmz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jmz RCSB], [http://www.ebi.ac.uk/pdbsum/4jmz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jmz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4jmz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
-	[[Category: Saccharomyces cerevisiae rm11-1a]]
	[[Category: Barelier, S]]		[[Category: Barelier, S]]
	[[Category: Fischer, M]]		[[Category: Fischer, M]]

OCA at 13:25, 4 January 2015

OCA — Sun, 04 Jan 2015 13:25:21 GMT

←Older revision		Revision as of 13:25, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4jmz\| PDB=4jmz \| SCENE= }}~~	+	==Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine==
-	===Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine===	+	<StructureSection load='4jmz' size='340' side='right' caption='[[4jmz]], [[Resolution\|resolution]] 1.82Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23874896}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4jmz]] is a 1 chain structure with sequence from [http://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=4JMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JMZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1M2:N-METHYL-1H-BENZIMIDAZOL-2-AMINE'>1M2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kxn\|1kxn]], [[1kxm\|1kxm]], [[4jm5\|4jm5]], [[4jm6\|4jm6]], [[4jm8\|4jm8]], [[4jm9\|4jm9]], [[4jma\|4jma]], [[4jmw\|4jmw]], [[4jpl\|4jpl]], [[4jpt\|4jpt]], [[4jpu\|4jpu]], [[4jqj\|4jqj]], [[4jqk\|4jqk]], [[4jqm\|4jqm]], [[4jqn\|4jqn]], [[4jmb\|4jmb]], [[4jms\|4jms]], [[4jmt\|4jmt]], [[4jmv\|4jmv]], [[4jn0\|4jn0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP1 CCP CPO YKR066C, SCRG_04081 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285006 Saccharomyces cerevisiae RM11-1a])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=4jmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jmz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jmz RCSB], [http://www.ebi.ac.uk/pdbsum/4jmz PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A key challenge in structure-based discovery is accounting for modulation of protein-ligand interactions by ordered and bulk solvent. To investigate this, we compared ligand binding to a buried cavity in Cytochrome c Peroxidase (CcP), where affinity is dominated by a single ionic interaction, versus a cavity variant partly opened to solvent by loop deletion. This opening had unexpected effects on ligand orientation, affinity, and ordered water structure. Some ligands lost over ten-fold in affinity and reoriented in the cavity, while others retained their geometries, formed new interactions with water networks, and improved affinity. To test our ability to discover new ligands against this opened site prospectively, a 534,000 fragment library was docked against the open cavity using two models of ligand solvation. Using an older solvation model that prioritized many neutral molecules, three such uncharged docking hits were tested, none of which was observed to bind; these molecules were not highly ranked by the new, context-dependent solvation score. Using this new method, another 15 highly-ranked molecules were tested for binding. In contrast to the previous result, 14 of these bound detectably, with affinities ranging from 8 microM to 2 mM. In crystal structures, four of these new ligands superposed well with the docking predictions but two did not, reflecting unanticipated interactions with newly ordered waters molecules. Comparing recognition between this open cavity and its buried analog begins to isolate the roles of ordered solvent in a system that lends itself readily to prospective testing and that may be broadly useful to the community.

-	~~==About this Structure==~~	+	Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities.,Barelier S, Boyce SE, Fish I, Fischer M, Goodin DB, Shoichet BK PLoS One. 2013 Jul 18;8(7):e69153. doi: 10.1371/journal.pone.0069153. Print 2013. PMID:23874896<ref>PMID:23874896</ref>
-	~~[[4jmz]] is a 1 chain structure with sequence from [http~~:~~//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=4JMZ OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]		*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023874896</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae rm11-1a]]		[[Category: Saccharomyces cerevisiae rm11-1a]]
-	[[Category: Barelier, S.]]	+	[[Category: Barelier, S]]
-	[[Category: Fischer, M.]]	+	[[Category: Fischer, M]]
	[[Category: Bulk solvent]]		[[Category: Bulk solvent]]
	[[Category: Docking]]		[[Category: Docking]]

OCA at 05:56, 28 August 2013

OCA — Wed, 28 Aug 2013 05:56:21 GMT

←Older revision		Revision as of 05:56, 28 August 2013
Line 1:		Line 1:
	{{STRUCTURE_4jmz\| PDB=4jmz \| SCENE= }}		{{STRUCTURE_4jmz\| PDB=4jmz \| SCENE= }}
	===Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine===		===Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine===
		+	{{ABSTRACT_PUBMED_23874896}}

	==About this Structure==		==About this Structure==
	[[4jmz]] is a 1 chain structure with sequence from [http://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=4JMZ OCA].		[[4jmz]] is a 1 chain structure with sequence from [http://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=4JMZ OCA].
		+
		+	==See Also==
		+	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023874896</ref><references group="xtra"/><references/>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae rm11-1a]]		[[Category: Saccharomyces cerevisiae rm11-1a]]

OCA at 07:56, 2 May 2013

OCA — Thu, 02 May 2013 07:56:09 GMT

←Older revision		Revision as of 07:56, 2 May 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4jmz\| PDB=4jmz \| SCENE= }}
		+	===Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with N-methyl-1H-benzimidazol-2-amine===

-	~~The entry~~ 4jmz is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4jmz]] is a 1 chain structure with sequence from [http://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=4JMZ OCA].
-	~~Authors~~: Barelier, S., Fischer, M.	+	[[Category: Cytochrome-c peroxidase]]
-		+	[[Category: Saccharomyces cerevisiae rm11-1a]]
-	~~Description~~:	+	[[Category: Barelier, S.]]
		+	[[Category: Fischer, M.]]
		+	[[Category: Bulk solvent]]
		+	[[Category: Docking]]
		+	[[Category: Ligand binding]]
		+	[[Category: Model system]]
		+	[[Category: Ordered water]]
		+	[[Category: Oxidoreductase]]

OCA at 00:55, 4 April 2013

OCA — Thu, 04 Apr 2013 00:55:59 GMT

←Older revision		Revision as of 00:55, 4 April 2013
Line 5:		Line 5:
	Authors: Barelier, S., Fischer, M.		Authors: Barelier, S., Fischer, M.

-	Description: ~~Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with ZINC00039693~~	+	Description:

OCA: Protected "4jmz" [edit=sysop:move=sysop]

OCA — Wed, 20 Mar 2013 16:24:04 GMT

Protected "4jmz" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:24, 20 March 2013

OCA: New page: '''Unreleased structure''' The entry 4jmz is ON HOLD Authors: Barelier, S., Fischer, M. Description: Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with ZINC000...

OCA — Wed, 20 Mar 2013 16:24:03 GMT

New page: '''Unreleased structure''' The entry 4jmz is ON HOLD Authors: Barelier, S., Fischer, M. Description: Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with ZINC000...

New page

'''Unreleased structure'''

The entry 4jmz is ON HOLD

Authors: Barelier, S., Fischer, M.

Description: Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with ZINC00039693