2eus - Revision history

OCA at 07:59, 13 August 2026

2026-08-13T07:59:30Z

← Older revision		Revision as of 07:59, 13 August 2026
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eu/2eus_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eu/2eus_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 07:39, 23 August 2023

2023-08-23T07:39:52Z

← Older revision		Revision as of 07:39, 23 August 2023
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	<StructureSection load='2eus' size='340' side='right'caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2eus' size='340' side='right'caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EUS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EUS FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ABN:BENZYLAMINE'>ABN</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]] 1.55Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABN:BENZYLAMINE'>ABN</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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [https://pdbe.org/2eus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [https://www.ebi.ac.uk/pdbsum/2eus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eus 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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [https://pdbe.org/2eus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [https://www.ebi.ac.uk/pdbsum/2eus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eus ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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.		[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: Atcc 18824]]~~
	~~[[Category: Cytochrome-c peroxidase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Boyce, S E~~]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: ~~Brenk, R~~]]		[[Category: Boyce SE]]
	[[Category: ~~Goodin, D B~~]]		[[Category: Brenk R]]
	[[Category: ~~Shoichet, B K~~]]		[[Category: Goodin DB]]
	[[Category: ~~Vetter, S W~~]]		[[Category: Shoichet BK]]
	[[Category: ~~Engineered ligand binding site]]~~		[[Category: Vetter SW]]
	~~[[Category: Oxidoreductase~~]]

OCA at 17:18, 20 October 2021

2021-10-20T17:18:47Z

← Older revision		Revision as of 17:18, 20 October 2021
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	<StructureSection load='2eus' size='340' side='right'caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2eus' size='340' side='right'caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2EUS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EUS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABN:BENZYLAMINE'>ABN</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=ABN:BENZYLAMINE'>ABN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [~~http~~://pdbe.org/2eus PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2eus PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2eus 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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [https://pdbe.org/2eus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [https://www.ebi.ac.uk/pdbsum/2eus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eus ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.		[[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]]

OCA at 10:42, 18 March 2020

2020-03-18T10:42:01Z

← Older revision		Revision as of 10:42, 18 March 2020
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	==Cytochrome c peroxidase (CCP) in complex with benzylamine==		==Cytochrome c peroxidase (CCP) in complex with benzylamine==
	<StructureSection load='2eus' size='340' side='right' caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2eus' size='340' side='right'caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUS FirstGlance]. <br>
Line 31:		Line 31:

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]		*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
			[[Category: Large Structures]]
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]
	[[Category: Brenk, R]]		[[Category: Brenk, R]]

OCA at 08:51, 14 June 2018

2018-06-14T08:51:05Z

← Older revision		Revision as of 08:51, 14 June 2018
Line 1:		Line 1:

	==Cytochrome c peroxidase (CCP) in complex with benzylamine==		==Cytochrome c peroxidase (CCP) in complex with benzylamine==
	<StructureSection load='2eus' size='340' side='right' caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2eus' size='340' side='right' caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABN:BENZYLAMINE'>ABN</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=ABN:BENZYLAMINE'>ABN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [http://pdbe.org/2eus PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [http://www.ebi.ac.uk/pdbsum/2eus 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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [http://pdbe.org/2eus PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [http://www.ebi.ac.uk/pdbsum/2eus PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2eus ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/eu/2eus_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eu/2eus_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>

OCA at 02:36, 7 February 2016

2016-02-07T02:36:14Z

← Older revision		Revision as of 02:36, 7 February 2016
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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=2eus ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:51, 9 September 2015

2015-09-09T20:51:36Z

← Older revision		Revision as of 20:51, 9 September 2015
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	<StructureSection load='2eus' size='340' side='right' caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='2eus' size='340' side='right' caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure 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=2EUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABN:BENZYLAMINE'>ABN</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=ABN:BENZYLAMINE'>ABN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [http://www.ebi.ac.uk/pdbsum/2eus 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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [http://pdbe.org/2eus PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [http://www.ebi.ac.uk/pdbsum/2eus PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 2eus" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Atcc 18824]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	~~[[Category: Saccharomyces cerevisiae]]~~
	[[Category: Boyce, S E]]		[[Category: Boyce, S E]]
	[[Category: Brenk, R]]		[[Category: Brenk, R]]

OCA at 07:09, 24 December 2014

2014-12-24T07:09:46Z

← Older revision		Revision as of 07:09, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure 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=2EUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure 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=2EUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUS FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABN:BENZYLAMINE'>ABN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABN:BENZYLAMINE'>ABN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [http://www.ebi.ac.uk/pdbsum/2eus 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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [http://www.ebi.ac.uk/pdbsum/2eus PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://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]]
Line 34:		Line 36:
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Boyce, S E.]]		[[Category: Boyce, S E]]
	[[Category: Brenk, R.]]		[[Category: Brenk, R]]
	[[Category: Goodin, D B.]]		[[Category: Goodin, D B]]
	[[Category: Shoichet, B K.]]		[[Category: Shoichet, B K]]
	[[Category: Vetter, S W.]]		[[Category: Vetter, S W]]
	[[Category: Engineered ligand binding site]]		[[Category: Engineered ligand binding site]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 02:22, 29 September 2014

2014-09-29T02:22:27Z

← Older revision		Revision as of 02:22, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2eus~~.~~png~~\|~~left~~\|~~200px~~]]		==Cytochrome c peroxidase (CCP) in complex with benzylamine==
			<StructureSection load='2eus' size='340' side='right' caption='[[2eus]], [[Resolution\|resolution]] 1.55Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2eus]] is a 1 chain structure 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=2EUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EUS FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABN:BENZYLAMINE'>ABN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
			<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=2eus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eus OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eus RCSB], [http://www.ebi.ac.uk/pdbsum/2eus 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/eu/2eus_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 ==
			A model binding site was used to investigate charge-charge interactions in molecular docking. This simple site, a small (180A(3)) engineered cavity in cyctochrome c peroxidase (CCP), is negatively charged and completely buried from solvent, allowing us to explore the balance between electrostatic energy and ligand desolvation energy in a system where many of the common approximations in docking do not apply. A database with about 5300 molecules was docked into this cavity. Retrospective testing with known ligands and decoys showed that overall the balance between electrostatic interaction and desolvation energy was captured. More interesting were prospective docking scre"ens that looked for novel ligands, especially those that might reveal problems with the docking and energy methods. Based on screens of the 5300 compound database, both high-scoring and low-scoring molecules were acquired and tested for binding. Out of 16 new, high-scoring compounds tested, 15 were observed to bind. All of these were small heterocyclic cations. Binding constants were measured for a few of these, they ranged between 20microM and 60microM. Crystal structures were determined for ten of these ligands in complex with the protein. The observed ligand geometry corresponded closely to that predicted by docking. Several low-scoring alkyl amino cations were also tested and found to bind. The low docking score of these molecules owed to the relatively high charge density of the charged amino group and the corresponding high desolvation penalty. When the complex structures of those ligands were determined, a bound water molecule was observed interacting with the amino group and a backbone carbonyl group of the cavity. This water molecule mitigates the desolvation penalty and improves the interaction energy relative to that of the "naked" site used in the docking screen. Finally, six low-scoring neutral molecules were also tested, with a view to looking for false negative predictions. Whereas most of these did not bind, two did (phenol and 3-fluorocatechol). Crystal structures for these two ligands in complex with the cavity site suggest reasons for their binding. That these neutral molecules do, in fact bind, contradicts previous results in this site and, along with the alkyl amines, provides instructive false negatives that help identify weaknesses in our scoring functions. Several improvements of these are considered.

	~~{{STRUCTURE_2eus\| PDB=2eus \| SCENE= }}~~		Probing molecular docking in a charged model binding site.,Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK J Mol Biol. 2006 Apr 14;357(5):1449-70. Epub 2006 Feb 2. PMID:16490206<ref>PMID:16490206</ref>

	~~===Cytochrome c peroxidase (CCP) in complex with benzylamine===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16490206}}~~

	~~==About this Structure==~~
	~~[[2eus]] is~~ a ~~1 chain structure 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=2EUS OCA].~~

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]		*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016490206<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 05:21, 20 October 2012

2012-10-20T05:21:36Z

← Older revision		Revision as of 05:21, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2eus]] 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=2EUS OCA].		[[2eus]] is a 1 chain structure 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=2EUS OCA].

	==See Also==		==See Also==