2rbz - Revision history

OCA at 11:53, 30 August 2023

2023-08-30T11:53:36Z

←Older revision		Revision as of 11:53, 30 August 2023
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	<StructureSection load='2rbz' size='340' side='right'caption='[[2rbz]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2rbz' size='340' side='right'caption='[[2rbz]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rbz]] is a 1 chain structure with sequence from [https://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=2RBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rbz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_YJM789 Saccharomyces cerevisiae YJM789]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RBZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=282:3~~-~~METHOXYPYRIDINE'>282</scene>~~, ~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1ac4\|1ac4]], [[2rbt\|2rbt]], [[2rbu\|2rbu]], [[2rbv\|2rbv]], [[2rbw\|2rbw]], [[2rbx\|2rbx]], [[2rby\|2rby]], [[2rc0\|2rc0]], [[2rc1\|2rc1]], [[2rc2\|2rc2]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=282:3-METHOXYPYRIDINE'>282</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ccp1~~, ~~ccp, cpo ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 Baker's yeast])~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [https://pdbe.org/2rbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [https://www.ebi.ac.uk/pdbsum/2rbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbz 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=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [https://pdbe.org/2rbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [https://www.ebi.ac.uk/pdbsum/2rbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
-	[[Category: Cytochrome-c peroxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Boyce, S E~~]]	+	[[Category: Saccharomyces cerevisiae YJM789]]
-	[[Category: ~~Graves, A P~~]]	+	[[Category: Boyce SE]]
-	[[Category: ~~Shoichet, B K~~]]	+	[[Category: Graves AP]]
-	[[Category: ~~Oxidoreductase~~]]	+	[[Category: Shoichet BK]]

OCA at 04:21, 2 July 2021

2021-07-02T04:21:03Z

←Older revision		Revision as of 04:21, 2 July 2021
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	==Cytochrome C Peroxidase W191G in complex 3-methoxypyridine==		==Cytochrome C Peroxidase W191G in complex 3-methoxypyridine==
-	<StructureSection load='2rbz' size='340' side='right' caption='[[2rbz]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2rbz' size='340' side='right'caption='[[2rbz]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rbz]] 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=2RBZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rbz]] is a 1 chain structure with sequence from [https://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=2RBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RBZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=282:3-METHOXYPYRIDINE'>282</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=282:3-METHOXYPYRIDINE'>282</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ac4\|1ac4]], [[2rbt\|2rbt]], [[2rbu\|2rbu]], [[2rbv\|2rbv]], [[2rbw\|2rbw]], [[2rbx\|2rbx]], [[2rby\|2rby]], [[2rc0\|2rc0]], [[2rc1\|2rc1]], [[2rc2\|2rc2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ac4\|1ac4]], [[2rbt\|2rbt]], [[2rbu\|2rbu]], [[2rbv\|2rbv]], [[2rbw\|2rbw]], [[2rbx\|2rbx]], [[2rby\|2rby]], [[2rc0\|2rc0]], [[2rc1\|2rc1]], [[2rc2\|2rc2]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccp1, ccp, cpo ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 Baker's yeast])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccp1, ccp, cpo ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 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'>[https://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [https://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=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [~~http~~://pdbe.org/2rbz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rbz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbz 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=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [https://pdbe.org/2rbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [https://www.ebi.ac.uk/pdbsum/2rbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbz ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rb/2rbz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rb/2rbz_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2rbz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2rbz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
		+	[[Category: Large Structures]]
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]
	[[Category: Graves, A P]]		[[Category: Graves, A P]]
	[[Category: Shoichet, B K]]		[[Category: Shoichet, B K]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 07:48, 25 October 2017

2017-10-25T07:48:05Z

←Older revision		Revision as of 07:48, 25 October 2017
Line 1:		Line 1:
		+
	==Cytochrome C Peroxidase W191G in complex 3-methoxypyridine==		==Cytochrome C Peroxidase W191G in complex 3-methoxypyridine==
	<StructureSection load='2rbz' size='340' side='right' caption='[[2rbz]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2rbz' size='340' side='right' caption='[[2rbz]], [[Resolution\|resolution]] 1.80Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccp1, ccp, cpo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 Baker's yeast])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccp1, ccp, cpo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 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=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [http://pdbe.org/2rbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [http://www.ebi.ac.uk/pdbsum/2rbz 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=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [http://pdbe.org/2rbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [http://www.ebi.ac.uk/pdbsum/2rbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbz ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 2rbz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2rbz" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:14, 7 February 2016

2016-02-07T12:14:11Z

←Older revision		Revision as of 12:14, 7 February 2016
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	<StructureSection load='2rbz' size='340' side='right' caption='[[2rbz]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2rbz' size='340' side='right' caption='[[2rbz]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rbz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae_yjm789 Saccharomyces cerevisiae yjm789~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rbz]] 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=2RBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=282:3-METHOXYPYRIDINE'>282</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=282:3-METHOXYPYRIDINE'>282</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ac4\|1ac4]], [[2rbt\|2rbt]], [[2rbu\|2rbu]], [[2rbv\|2rbv]], [[2rbw\|2rbw]], [[2rbx\|2rbx]], [[2rby\|2rby]], [[2rc0\|2rc0]], [[2rc1\|2rc1]], [[2rc2\|2rc2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ac4\|1ac4]], [[2rbt\|2rbt]], [[2rbu\|2rbu]], [[2rbv\|2rbv]], [[2rbw\|2rbw]], [[2rbx\|2rbx]], [[2rby\|2rby]], [[2rc0\|2rc0]], [[2rc1\|2rc1]], [[2rc2\|2rc2]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccp1, ccp, cpo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 ~~Saccharomyces cerevisiae YJM789~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccp1, ccp, cpo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 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=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [http://www.ebi.ac.uk/pdbsum/2rbz 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=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [http://pdbe.org/2rbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [http://www.ebi.ac.uk/pdbsum/2rbz PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rbz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 2rbz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
-	[[Category: Saccharomyces cerevisiae yjm789]]
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]
	[[Category: Graves, A P]]		[[Category: Graves, A P]]
	[[Category: Shoichet, B K]]		[[Category: Shoichet, B K]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 14:46, 19 January 2015

2015-01-19T14:46:33Z

←Older revision		Revision as of 14:46, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rbz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_yjm789 Saccharomyces cerevisiae yjm789]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rbz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_yjm789 Saccharomyces cerevisiae yjm789]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=282:3-METHOXYPYRIDINE'>282</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=282:3-METHOXYPYRIDINE'>282</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ac4\|1ac4]], [[2rbt\|2rbt]], [[2rbu\|2rbu]], [[2rbv\|2rbv]], [[2rbw\|2rbw]], [[2rbx\|2rbx]], [[2rby\|2rby]], [[2rc0\|2rc0]], [[2rc1\|2rc1]], [[2rc2\|2rc2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ac4\|1ac4]], [[2rbt\|2rbt]], [[2rbu\|2rbu]], [[2rbv\|2rbv]], [[2rbw\|2rbw]], [[2rbx\|2rbx]], [[2rby\|2rby]], [[2rc0\|2rc0]], [[2rc1\|2rc1]], [[2rc2\|2rc2]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccp1, ccp, cpo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 Saccharomyces cerevisiae YJM789])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccp1, ccp, cpo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 Saccharomyces cerevisiae YJM789])</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [http://www.ebi.ac.uk/pdbsum/2rbz 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=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [http://www.ebi.ac.uk/pdbsum/2rbz PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae yjm789]]		[[Category: Saccharomyces cerevisiae yjm789]]
-	[[Category: Boyce, S E.]]	+	[[Category: Boyce, S E]]
-	[[Category: Graves, A P.]]	+	[[Category: Graves, A P]]
-	[[Category: Shoichet, B K.]]	+	[[Category: Shoichet, B K]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 07:17, 29 September 2014

2014-09-29T07:17:37Z

←Older revision		Revision as of 07:17, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2rbz.~~png~~\|~~left~~\|200px]]	+	==Cytochrome C Peroxidase W191G in complex 3-methoxypyridine==
		+	<StructureSection load='2rbz' size='340' side='right' caption='[[2rbz]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rbz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_yjm789 Saccharomyces cerevisiae yjm789]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RBZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=282:3-METHOXYPYRIDINE'>282</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ac4\|1ac4]], [[2rbt\|2rbt]], [[2rbu\|2rbu]], [[2rbv\|2rbv]], [[2rbw\|2rbw]], [[2rbx\|2rbx]], [[2rby\|2rby]], [[2rc0\|2rc0]], [[2rc1\|2rc1]], [[2rc2\|2rc2]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ccp1, ccp, cpo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=307796 Saccharomyces cerevisiae YJM789])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rbz RCSB], [http://www.ebi.ac.uk/pdbsum/2rbz PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rb/2rbz_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Molecular docking computationally screens thousands to millions of organic molecules against protein structures, looking for those with complementary fits. Many approximations are made, often resulting in low "hit rates." A strategy to overcome these approximations is to rescore top-ranked docked molecules using a better but slower method. One such is afforded by molecular mechanics-generalized Born surface area (MM-GBSA) techniques. These more physically realistic methods have improved models for solvation and electrostatic interactions and conformational change compared to most docking programs. To investigate MM-GBSA rescoring, we re-ranked docking hit lists in three small buried sites: a hydrophobic cavity that binds apolar ligands, a slightly polar cavity that binds aryl and hydrogen-bonding ligands, and an anionic cavity that binds cationic ligands. These sites are simple; consequently, incorrect predictions can be attributed to particular errors in the method, and many likely ligands may actually be tested. In retrospective calculations, MM-GBSA techniques with binding-site minimization better distinguished the known ligands for each cavity from the known decoys compared to the docking calculation alone. This encouraged us to test rescoring prospectively on molecules that ranked poorly by docking but that ranked well when rescored by MM-GBSA. A total of 33 molecules highly ranked by MM-GBSA for the three cavities were tested experimentally. Of these, 23 were observed to bind--these are docking false negatives rescued by rescoring. The 10 remaining molecules are true negatives by docking and false positives by MM-GBSA. X-ray crystal structures were determined for 21 of these 23 molecules. In many cases, the geometry prediction by MM-GBSA improved the initial docking pose and more closely resembled the crystallographic result; yet in several cases, the rescored geometry failed to capture large conformational changes in the protein. Intriguingly, rescoring not only rescued docking false positives, but also introduced several new false positives into the top-ranking molecules. We consider the origins of the successes and failures in MM-GBSA rescoring in these model cavity sites and the prospects for rescoring in biologically relevant targets.

-	~~{{STRUCTURE_2rbz\| PDB=2rbz \| SCENE= }}~~	+	Rescoring docking hit lists for model cavity sites: predictions and experimental testing.,Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK J Mol Biol. 2008 Mar 28;377(3):914-34. Epub 2008 Jan 30. PMID:18280498<ref>PMID:18280498</ref>

-	~~===Cytochrome C Peroxidase W191G in complex 3-methoxypyridine===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18280498}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2rbz]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae_yjm789 Saccharomyces cerevisiae yjm789]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]		*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018280498<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae yjm789]]		[[Category: Saccharomyces cerevisiae yjm789]]

OCA at 06:36, 20 October 2012

2012-10-20T06:36:25Z

←Older revision		Revision as of 06:36, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2rbz]] is a 1 chain structure ~~of [[Cytochrome c peroxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae~~ Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA].	+	[[2rbz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_yjm789 Saccharomyces cerevisiae yjm789]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA].

	==See Also==		==See Also==
Line 16:		Line 16:
	<ref group="xtra">PMID:018280498</ref><references group="xtra"/>		<ref group="xtra">PMID:018280498</ref><references group="xtra"/>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
-	[[Category: Saccharomyces cerevisiae]]	+	[[Category: Saccharomyces cerevisiae yjm789]]
	[[Category: Boyce, S E.]]		[[Category: Boyce, S E.]]
	[[Category: Graves, A P.]]		[[Category: Graves, A P.]]
	[[Category: Shoichet, B K.]]		[[Category: Shoichet, B K.]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA: Protected "2rbz" [edit=sysop:move=sysop]

2012-07-25T13:43:25Z

Protected "2rbz" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:43, 25 July 2012

OCA at 13:43, 25 July 2012

2012-07-25T13:43:23Z

←Older revision		Revision as of 13:43, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2rbz.png\|left\|200px]]		[[Image:2rbz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rbz", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2rbz\| PDB=2rbz \| SCENE= }}		{{STRUCTURE_2rbz\| PDB=2rbz \| SCENE= }}

	===Cytochrome C Peroxidase W191G in complex 3-methoxypyridine===		===Cytochrome C Peroxidase W191G in complex 3-methoxypyridine===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18280498}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18280498 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18280498}}		{{ABSTRACT_PUBMED_18280498}}

	==About this Structure==		==About this Structure==
-	~~2RBZ~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA].	+	[[2rbz]] is a 1 chain structure of [[Cytochrome c peroxidase]] with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA].
		+
		+	==See Also==
		+	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18280498~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018280498</ref><references group="xtra"/>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
Line 30:		Line 21:
	[[Category: Shoichet, B K.]]		[[Category: Shoichet, B K.]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:44:00 2009''

OCA at 11:44, 16 February 2009

2009-02-16T11:44:02Z

←Older revision		Revision as of 11:44, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2RBZ is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA].	+	2RBZ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RBZ OCA].

	==Reference==		==Reference==
-	Rescoring docking hit lists for model cavity sites: predictions and experimental testing., Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK, J Mol Biol. 2008 Mar 28;377(3):914-34. Epub 2008 Jan 30. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18280498 18280498]~~	+	<ref group="xtra">PMID:18280498</ref><references group="xtra"/>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Single protein]]
	[[Category: Boyce, S E.]]		[[Category: Boyce, S E.]]
	[[Category: Graves, A P.]]		[[Category: Graves, A P.]]
Line 32:		Line 31:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27~~ 16:14:~~12 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:44:00 2009''