2pes - Revision history

OCA at 09:09, 21 February 2024

OCA — Wed, 21 Feb 2024 09:09:14 GMT

←Older revision		Revision as of 09:09, 21 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pes]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PES FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pes]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PES FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AZA:8~~-~~AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2~~,6~~-DICARBOXYLIC+ACID'>PDC</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]] 1.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3]~~ </~~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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [https://pdbe.org/2pes PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [https://www.ebi.ac.uk/pdbsum/2pes PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pes 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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [https://pdbe.org/2pes PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [https://www.ebi.ac.uk/pdbsum/2pes PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pes ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/URIC_ASPFL URIC_ASPFL]] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.	+	[https://www.uniprot.org/uniprot/URIC_ASPFL URIC_ASPFL] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=2pes 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=2pes ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Tris-dipicolinate lanthanide complexes were used to prepare derivative crystals of six proteins: hen egg-white lysozyme, turkey egg-white lysozyme, thaumatin from Thaumatococcus daniellii, urate oxidase from Aspergillus flavus, porcine pancreatic elastase and xylanase from Trichoderma reesei. Diffraction data were collected using either synchrotron radiation or X-rays from a laboratory source. In all cases, the complex turned out to be bound to the protein and the phases determined using the anomalous scattering of the lanthanide led to high-quality electron-density maps. The binding mode of the complex was characterized from the refined structures. The lanthanide tris-dipicolinate was found to bind through interactions between carboxylate groups of the dipicolinate ligands and hydrogen-bond donor groups of the protein. In each binding site, one enantiomeric form of the complex is selected from the racemic solution according to the specific site topology. For hen egg-white lysozyme and xylanase, derivative crystals obtained by cocrystallization belonged to a new monoclinic C2 crystal form that diffracted to high resolution.
-
-	A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction.,Pompidor G, Maury O, Vicat J, Kahn R Acta Crystallogr D Biol Crystallogr. 2010 Jul;66(Pt 7):762-9. Epub 2010, Jun 19. PMID:20606256<ref>PMID:20606256</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2pes" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Urate ~~Oxidase~~\|Urate ~~Oxidase~~]]	+	*[[Urate oxidase 3D structures\|Urate oxidase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Aspergillus flavus]]		[[Category: Aspergillus flavus]]
-	[[Category: Factor independent urate hydroxylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kahn, R]]	+	[[Category: Kahn R]]
-	[[Category: Pompidor, G]]	+	[[Category: Pompidor G]]
-	[[Category: Vicat, J]]	+	[[Category: Vicat J]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Urate oxidase tris-dipicolinate lutetium 8-azaxanthin x-ray~~]]	+

OCA at 07:45, 9 March 2022

OCA — Wed, 09 Mar 2022 07:45:14 GMT

←Older revision		Revision as of 07:45, 9 March 2022
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	<StructureSection load='2pes' size='340' side='right'caption='[[2pes]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2pes' size='340' side='right'caption='[[2pes]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pes]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2PES FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pes]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PES FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [~~http~~://pdbe.org/2pes PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pes PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pes 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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [https://pdbe.org/2pes PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [https://www.ebi.ac.uk/pdbsum/2pes PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pes ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/URIC_ASPFL URIC_ASPFL]] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.	+	[[https://www.uniprot.org/uniprot/URIC_ASPFL URIC_ASPFL]] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:54, 3 June 2020

OCA — Wed, 03 Jun 2020 06:54:45 GMT

←Older revision		Revision as of 06:54, 3 June 2020
Line 1:		Line 1:

	==Urate Oxidase in complex with tris-dipicolinate Lutetium==		==Urate Oxidase in complex with tris-dipicolinate Lutetium==
-	<StructureSection load='2pes' size='340' side='right' caption='[[2pes]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='2pes' size='340' side='right'caption='[[2pes]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pes]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PES FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pes]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2PES FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [http://pdbe.org/2pes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [http://www.ebi.ac.uk/pdbsum/2pes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pes ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [http://pdbe.org/2pes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [http://www.ebi.ac.uk/pdbsum/2pes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pes ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 39:		Line 39:
	[[Category: Aspergillus flavus]]		[[Category: Aspergillus flavus]]
	[[Category: Factor independent urate hydroxylase]]		[[Category: Factor independent urate hydroxylase]]
		+	[[Category: Large Structures]]
	[[Category: Kahn, R]]		[[Category: Kahn, R]]
	[[Category: Pompidor, G]]		[[Category: Pompidor, G]]

OCA at 08:20, 29 August 2018

OCA — Wed, 29 Aug 2018 08:20:28 GMT

←Older revision		Revision as of 08:20, 29 August 2018
Line 1:		Line 1:
		+
	==Urate Oxidase in complex with tris-dipicolinate Lutetium==		==Urate Oxidase in complex with tris-dipicolinate Lutetium==
	<StructureSection load='2pes' size='340' side='right' caption='[[2pes]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2pes' size='340' side='right' caption='[[2pes]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [http://pdbe.org/2pes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [http://www.ebi.ac.uk/pdbsum/2pes 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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [http://pdbe.org/2pes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [http://www.ebi.ac.uk/pdbsum/2pes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pes ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/2pes_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/2pes_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 07:21, 9 February 2016

OCA — Tue, 09 Feb 2016 07:21:47 GMT

←Older revision		Revision as of 07:21, 9 February 2016
Line 18:		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=2pes ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:55, 10 September 2015

OCA — Thu, 10 Sep 2015 19:55:21 GMT

←Older revision		Revision as of 19:55, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Urate_oxidase Urate oxidase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Factor_independent_urate_hydroxylase Factor independent urate hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [http://www.ebi.ac.uk/pdbsum/2pes 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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [http://pdbe.org/2pes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [http://www.ebi.ac.uk/pdbsum/2pes PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2pes" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Aspergillus flavus]]		[[Category: Aspergillus flavus]]
-	[[Category: ~~Urate oxidase~~]]	+	[[Category: Factor independent urate hydroxylase]]
	[[Category: Kahn, R]]		[[Category: Kahn, R]]
	[[Category: Pompidor, G]]		[[Category: Pompidor, G]]

OCA at 05:19, 25 December 2014

OCA — Thu, 25 Dec 2014 05:19:13 GMT

←Older revision		Revision as of 05:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pes]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PES FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pes]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PES FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urate_oxidase Urate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urate_oxidase Urate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [http://www.ebi.ac.uk/pdbsum/2pes 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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [http://www.ebi.ac.uk/pdbsum/2pes PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/URIC_ASPFL URIC_ASPFL]] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Aspergillus flavus]]		[[Category: Aspergillus flavus]]
	[[Category: Urate oxidase]]		[[Category: Urate oxidase]]
-	[[Category: Kahn, R.]]	+	[[Category: Kahn, R]]
-	[[Category: Pompidor, G.]]	+	[[Category: Pompidor, G]]
-	[[Category: Vicat, J.]]	+	[[Category: Vicat, J]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Urate oxidase tris-dipicolinate lutetium 8-azaxanthin x-ray]]		[[Category: Urate oxidase tris-dipicolinate lutetium 8-azaxanthin x-ray]]

OCA at 07:21, 29 September 2014

OCA — Mon, 29 Sep 2014 07:21:11 GMT

←Older revision		Revision as of 07:21, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2pes.~~png~~\|~~left~~\|200px]]	+	==Urate Oxidase in complex with tris-dipicolinate Lutetium==
		+	<StructureSection load='2pes' size='340' side='right' caption='[[2pes]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pes]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PES FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1r51\|1r51]], [[2pc2\|2pc2]], [[2pe7\|2pe7]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urate_oxidase Urate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.3 1.7.3.3] </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=2pes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pes OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pes RCSB], [http://www.ebi.ac.uk/pdbsum/2pes 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/pe/2pes_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 ==
		+	Tris-dipicolinate lanthanide complexes were used to prepare derivative crystals of six proteins: hen egg-white lysozyme, turkey egg-white lysozyme, thaumatin from Thaumatococcus daniellii, urate oxidase from Aspergillus flavus, porcine pancreatic elastase and xylanase from Trichoderma reesei. Diffraction data were collected using either synchrotron radiation or X-rays from a laboratory source. In all cases, the complex turned out to be bound to the protein and the phases determined using the anomalous scattering of the lanthanide led to high-quality electron-density maps. The binding mode of the complex was characterized from the refined structures. The lanthanide tris-dipicolinate was found to bind through interactions between carboxylate groups of the dipicolinate ligands and hydrogen-bond donor groups of the protein. In each binding site, one enantiomeric form of the complex is selected from the racemic solution according to the specific site topology. For hen egg-white lysozyme and xylanase, derivative crystals obtained by cocrystallization belonged to a new monoclinic C2 crystal form that diffracted to high resolution.

-	~~{{STRUCTURE_2pes\| PDB=2pes \| SCENE= }}~~	+	A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction.,Pompidor G, Maury O, Vicat J, Kahn R Acta Crystallogr D Biol Crystallogr. 2010 Jul;66(Pt 7):762-9. Epub 2010, Jun 19. PMID:20606256<ref>PMID:20606256</ref>

-	~~===Urate Oxidase in complex with tris-dipicolinate Lutetium===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20606256}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2pes]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aspergillus_flavus Aspergillus flavus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA].~~	+

	==See Also==		==See Also==
	*[[Urate Oxidase\|Urate Oxidase]]		*[[Urate Oxidase\|Urate Oxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020606256<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Aspergillus flavus]]		[[Category: Aspergillus flavus]]
	[[Category: Urate oxidase]]		[[Category: Urate oxidase]]

OCA at 13:05, 20 October 2012

OCA — Sat, 20 Oct 2012 13:05:47 GMT

←Older revision		Revision as of 13:05, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2pes]] is a 1 chain structure ~~of [[Urate Oxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA].	+	[[2pes]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PES OCA].

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

OCA at 10:53, 26 July 2012

OCA — Thu, 26 Jul 2012 10:53:38 GMT

←Older revision		Revision as of 10:53, 26 July 2012
Line 1:		Line 1:
	[[Image:2pes.png\|left\|200px]]		[[Image:2pes.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2pes", 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_2pes\| PDB=2pes \| SCENE= }}		{{STRUCTURE_2pes\| PDB=2pes \| SCENE= }}

	===Urate Oxidase in complex with tris-dipicolinate Lutetium===		===Urate Oxidase in complex with tris-dipicolinate Lutetium===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20606256}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20606256 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20606256}}		{{ABSTRACT_PUBMED_20606256}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Urate Oxidase]]	+	*[[Urate Oxidase\|Urate Oxidase]]

	==Reference==		==Reference==