3b3w - Revision history

OCA at 12:01, 30 August 2023

OCA — Wed, 30 Aug 2023 12:01:40 GMT

←Older revision		Revision as of 12:01, 30 August 2023
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	<StructureSection load='3b3w' size='340' side='right'caption='[[3b3w]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3b3w' size='340' side='right'caption='[[3b3w]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b3w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"aeromonas_proteolytica"_merkel_et_al._1964 "aeromonas proteolytica" merkel et al. 1964~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b3w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B3W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=LEU:LEUCINE'>LEU</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.75Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3b35\|3b35]], [[3b3c\|3b3c]], [[3b3s\|3b3s]], [[3b3t\|3b3t]], [[3b3v\|3b3v]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat">AAP ([https~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=671 "Aeromonas proteolytica" Merkel et al. 1964])</td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Bacterial_leucyl_aminopeptidase Bacterial leucyl aminopeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.10 3.4.11.10]~~ </~~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=3b3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3w OCA], [https://pdbe.org/3b3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b3w RCSB], [https://www.ebi.ac.uk/pdbsum/3b3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3w 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=3b3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3w OCA], [https://pdbe.org/3b3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b3w RCSB], [https://www.ebi.ac.uk/pdbsum/3b3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3w ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AMPX_VIBPR AMPX_VIBPR]
	== 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: Aeromonas proteolytica merkel et al. 1964]]
-	[[Category: Bacterial leucyl aminopeptidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ataie, N J~~]]	+	[[Category: Vibrio proteolyticus]]
-	[[Category: ~~Hoang, Q Q~~]]	+	[[Category: Ataie NJ]]
-	[[Category: ~~Milne, A~~]]	+	[[Category: Hoang QQ]]
-	[[Category: ~~Petsko, G~~ A]]	+	[[Category: Milne A]]
-	[[Category: ~~Ringe, D~~]]	+	[[Category: Petsko GA]]
-	[[Category: ~~Zahniser, M P.~~D]]	+	[[Category: Ringe D]]
-	[[Category: ~~Alpha beta]]~~	+	[[Category: Zahniser MPD]]
-	~~[[Category: Aminopeptidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Zinc]]~~	+
-	~~[[Category: Zymogen~~]]	+

OCA at 18:53, 20 October 2021

OCA — Wed, 20 Oct 2021 18:53:17 GMT

←Older revision		Revision as of 18:53, 20 October 2021
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	==Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine==		==Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine==
-	<StructureSection load='3b3w' size='340' side='right' caption='[[3b3w]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='3b3w' size='340' side='right'caption='[[3b3w]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b3w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"aeromonas_proteolytica"_merkel_et_al._1964 "aeromonas proteolytica" merkel et al. 1964]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3B3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b3w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"aeromonas_proteolytica"_merkel_et_al._1964 "aeromonas proteolytica" merkel et al. 1964]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B3W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b35\|3b35]], [[3b3c\|3b3c]], [[3b3s\|3b3s]], [[3b3t\|3b3t]], [[3b3v\|3b3v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3b35\|3b35]], [[3b3c\|3b3c]], [[3b3s\|3b3s]], [[3b3t\|3b3t]], [[3b3v\|3b3v]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAP ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=671 "Aeromonas proteolytica" Merkel et al. 1964])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=671 "Aeromonas proteolytica" Merkel et al. 1964])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Bacterial_leucyl_aminopeptidase Bacterial leucyl aminopeptidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.10 3.4.11.10] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Bacterial_leucyl_aminopeptidase Bacterial leucyl aminopeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.10 3.4.11.10] </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=3b3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3w OCA], [~~http~~://pdbe.org/3b3w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3b3w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3b3w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3w 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=3b3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3w OCA], [https://pdbe.org/3b3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b3w RCSB], [https://www.ebi.ac.uk/pdbsum/3b3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3w ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/3b3w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/3b3w_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 3b3w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3b3w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	[[Category: Aeromonas proteolytica merkel et al. 1964]]		[[Category: Aeromonas proteolytica merkel et al. 1964]]
	[[Category: Bacterial leucyl aminopeptidase]]		[[Category: Bacterial leucyl aminopeptidase]]
		+	[[Category: Large Structures]]
	[[Category: Ataie, N J]]		[[Category: Ataie, N J]]
	[[Category: Hoang, Q Q]]		[[Category: Hoang, Q Q]]

OCA at 07:55, 25 October 2017

OCA — Wed, 25 Oct 2017 07:55:11 GMT

←Older revision		Revision as of 07:55, 25 October 2017
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 3b3w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3b3w" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Aminopeptidase\|Aminopeptidase]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Protease]]		[[Category: Protease]]
	[[Category: Secreted]]		[[Category: Secreted]]
		+	[[Category: Zinc]]
	[[Category: Zymogen]]		[[Category: Zymogen]]

OCA at 09:19, 11 August 2016

OCA — Thu, 11 Aug 2016 09:19:51 GMT

←Older revision		Revision as of 09:19, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine==		==Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine==
	<StructureSection load='3b3w' size='340' side='right' caption='[[3b3w]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3b3w' size='340' side='right' caption='[[3b3w]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b3w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Vibrio_proteolyticus Vibrio proteolyticus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b3w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"aeromonas_proteolytica"_merkel_et_al._1964 "aeromonas proteolytica" merkel et al. 1964]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b35\|3b35]], [[3b3c\|3b3c]], [[3b3s\|3b3s]], [[3b3t\|3b3t]], [[3b3v\|3b3v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b35\|3b35]], [[3b3c\|3b3c]], [[3b3s\|3b3s]], [[3b3t\|3b3t]], [[3b3v\|3b3v]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=671 ~~Vibrio proteolyticus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=671 "Aeromonas proteolytica" Merkel et al. 1964])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Bacterial_leucyl_aminopeptidase Bacterial leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.10 3.4.11.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Bacterial_leucyl_aminopeptidase Bacterial leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.10 3.4.11.10] </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=3b3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b3w RCSB], [http://www.ebi.ac.uk/pdbsum/3b3w 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=3b3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3w OCA], [http://pdbe.org/3b3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b3w RCSB], [http://www.ebi.ac.uk/pdbsum/3b3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b3w ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 18:
	<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=3b3w 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 3b3w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aeromonas proteolytica merkel et al. 1964]]
	[[Category: Bacterial leucyl aminopeptidase]]		[[Category: Bacterial leucyl aminopeptidase]]
-	[[Category: Vibrio proteolyticus]]
	[[Category: Ataie, N J]]		[[Category: Ataie, N J]]
	[[Category: Hoang, Q Q]]		[[Category: Hoang, Q Q]]

OCA at 10:21, 20 January 2015

OCA — Tue, 20 Jan 2015 10:21:12 GMT

←Older revision		Revision as of 10:21, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3b3w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3W FirstGlance]. <br>		<table><tr><td colspan='2'>[[3b3w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b35\|3b35]], [[3b3c\|3b3c]], [[3b3s\|3b3s]], [[3b3t\|3b3t]], [[3b3v\|3b3v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b35\|3b35]], [[3b3c\|3b3c]], [[3b3s\|3b3s]], [[3b3t\|3b3t]], [[3b3v\|3b3v]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=671 Vibrio proteolyticus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=671 Vibrio proteolyticus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Bacterial_leucyl_aminopeptidase Bacterial leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.10 3.4.11.10] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Bacterial_leucyl_aminopeptidase Bacterial leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.10 3.4.11.10] </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=3b3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b3w RCSB], [http://www.ebi.ac.uk/pdbsum/3b3w 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=3b3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b3w RCSB], [http://www.ebi.ac.uk/pdbsum/3b3w 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: Bacterial leucyl aminopeptidase]]		[[Category: Bacterial leucyl aminopeptidase]]
	[[Category: Vibrio proteolyticus]]		[[Category: Vibrio proteolyticus]]
-	[[Category: Ataie, N J.]]	+	[[Category: Ataie, N J]]
-	[[Category: Hoang, Q Q.]]	+	[[Category: Hoang, Q Q]]
-	[[Category: Milne, A.]]	+	[[Category: Milne, A]]
-	[[Category: Petsko, G A.]]	+	[[Category: Petsko, G A]]
-	[[Category: Ringe, D.]]	+	[[Category: Ringe, D]]
-	[[Category: Zahniser, M P.D.]]	+	[[Category: Zahniser, M P.D]]
	[[Category: Alpha beta]]		[[Category: Alpha beta]]
	[[Category: Aminopeptidase]]		[[Category: Aminopeptidase]]

OCA at 08:41, 29 September 2014

OCA — Mon, 29 Sep 2014 08:41:17 GMT

←Older revision		Revision as of 08:41, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3b3w.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine==
		+	<StructureSection load='3b3w' size='340' side='right' caption='[[3b3w]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3b3w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B3W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b35\|3b35]], [[3b3c\|3b3c]], [[3b3s\|3b3s]], [[3b3t\|3b3t]], [[3b3v\|3b3v]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=671 Vibrio proteolyticus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Bacterial_leucyl_aminopeptidase Bacterial leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.10 3.4.11.10] </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=3b3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b3w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b3w RCSB], [http://www.ebi.ac.uk/pdbsum/3b3w 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/b3/3b3w_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 ==
		+	The chemical properties of zinc make it an ideal metal to study the role of coordination strain in enzymatic rate enhancement. The zinc ion and the protein residues that are bound directly to the zinc ion represent a functional charge/dipole complex, and polarization of this complex, which translates to coordination distortion, may tune electrophilicity, and hence, reactivity. Conserved protein residues outside of the charge/dipole complex, such as second-shell residues, may play a role in supporting the electronic strain produced as a consequence of functional polarization. To test the correlation between charge/dipole polarity and ligand binding affinity, structure-function studies were carried out on the dizinc aminopeptidase from Vibrio proteolyticus. Alanine substitutions of S228 and M180 resulted in catalytically diminished enzymes whose crystal structures show very little change in the positions of the metal ions and the protein residues. However, more detailed inspections of the crystal structures show small positional changes that account for differences in the zinc ion coordination geometry. Measurements of the binding affinity of leucine phosphonic acid, a transition state analogue, and leucine, a product, show a correlation between coordination geometry and ligand binding affinity. These results suggest that the coordination number and polarity may tune the electrophilicity of zinc. This may have provided the evolving enzyme with the ability to discriminate between reaction coordinate species.

-	~~{{STRUCTURE_3b3w\| PDB=3b3w \| SCENE= }}~~	+	Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus.,Ataie NJ, Hoang QQ, Zahniser MP, Tu Y, Milne A, Petsko GA, Ringe D Biochemistry. 2008 Jul 22;47(29):7673-83. Epub 2008 Jun 25. PMID:18576673<ref>PMID:18576673</ref>

-	~~===Crystal structure~~ of the ~~S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18576673}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3b3w]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA].~~	+

	==See Also==		==See Also==
	*[[Aminopeptidase\|Aminopeptidase]]		*[[Aminopeptidase\|Aminopeptidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018576673<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacterial leucyl aminopeptidase]]		[[Category: Bacterial leucyl aminopeptidase]]
	[[Category: Vibrio proteolyticus]]		[[Category: Vibrio proteolyticus]]

OCA at 18:47, 20 October 2012

OCA — Sat, 20 Oct 2012 18:47:12 GMT

←Older revision		Revision as of 18:47, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3b3w]] is a 1 chain structure ~~of [[Aminopeptidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA].	+	[[3b3w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA].

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

OCA: Protected "3b3w" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 05:14:02 GMT

Protected "3b3w" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:14, 27 July 2012

OCA at 05:14, 27 July 2012

OCA — Fri, 27 Jul 2012 05:14:01 GMT

←Older revision		Revision as of 05:14, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3b3w.png\|left\|200px]]		[[Image:3b3w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3b3w", 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_3b3w\| PDB=3b3w \| SCENE= }}		{{STRUCTURE_3b3w\| PDB=3b3w \| SCENE= }}

	===Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine===		===Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18576673}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18576673 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18576673}}		{{ABSTRACT_PUBMED_18576673}}

	==About this Structure==		==About this Structure==
-	~~3B3W~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA].	+	[[3b3w]] is a 1 chain structure of [[Aminopeptidase]] with sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA].
		+
		+	==See Also==
		+	*[[Aminopeptidase\|Aminopeptidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18576673~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018576673</ref><references group="xtra"/>
	[[Category: Bacterial leucyl aminopeptidase]]		[[Category: Bacterial leucyl aminopeptidase]]
	[[Category: Vibrio proteolyticus]]		[[Category: Vibrio proteolyticus]]
Line 38:		Line 29:
	[[Category: Protease]]		[[Category: Protease]]
	[[Category: Secreted]]		[[Category: Secreted]]
-	[[Category: Zinc]]
	[[Category: Zymogen]]		[[Category: Zymogen]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:28:51 2009''

OCA at 19:28, 17 February 2009

OCA — Tue, 17 Feb 2009 19:28:52 GMT

←Older revision		Revision as of 19:28, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3B3W is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA].	+	3B3W is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_proteolyticus Vibrio proteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B3W OCA].

	==Reference==		==Reference==
-	Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus., Ataie NJ, Hoang QQ, Zahniser MP, Tu Y, Milne A, Petsko GA, Ringe D, Biochemistry. 2008 Jul 22;47(29):7673-83. Epub 2008 Jun 25. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18576673 18576673]~~	+	<ref group="xtra">PMID:18576673</ref><references group="xtra"/>
	[[Category: Bacterial leucyl aminopeptidase]]		[[Category: Bacterial leucyl aminopeptidase]]
-	[[Category: Single protein]]
	[[Category: Vibrio proteolyticus]]		[[Category: Vibrio proteolyticus]]
	[[Category: Ataie, N J.]]		[[Category: Ataie, N J.]]
Line 42:		Line 41:
	[[Category: Zymogen]]		[[Category: Zymogen]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Aug 13 13~~:39:~~23 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:28:51 2009''