3i7v - Revision history

OCA at 15:56, 1 November 2023

2023-11-01T15:56:19Z

←Older revision		Revision as of 15:56, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3i7v' size='340' side='right'caption='[[3i7v]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3i7v' size='340' side='right'caption='[[3i7v]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i7v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aquae Aquae~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i7v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.95Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3i7u\|3i7u]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])~~</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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [https://pdbe.org/3i7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [https://www.ebi.ac.uk/pdbsum/3i7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7v 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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [https://pdbe.org/3i7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [https://www.ebi.ac.uk/pdbsum/3i7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O66548_AQUAE O66548_AQUAE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aquae~~]]	+	[[Category: Aquifex aeolicus VF5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jeyakanthan, J]]	+	[[Category: Jeyakanthan J]]
-	[[Category: Kanaujia~~, S P~~]]	+	[[Category: Kanaujia SP]]
-	[[Category: Kuramitsu, S]]	+	[[Category: Kuramitsu S]]
-	[[Category: Nakagawa, N]]	+	[[Category: Nakagawa N]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Sekar K]]
-	[[Category: Sekar, K]]	+	[[Category: Shinkai A]]
-	[[Category: Shinkai, A]]	+	[[Category: Yokoyama S]]
-	[[Category: Yokoyama, S]]	+
-	~~[[Category: Ap4a]]~~	+
-	~~[[Category: Diadenosine polyphosphate]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: National project on protein structural and functional analyse]]~~	+
-	~~[[Category: Nppsfa]]~~	+
-	~~[[Category: Nudix protein]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 11:00, 13 April 2022

2022-04-13T11:00:31Z

←Older revision		Revision as of 11:00, 13 April 2022
Line 1:		Line 1:

	==Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5==		==Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5==
-	<StructureSection load='3i7v' size='340' side='right' caption='[[3i7v]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='3i7v' size='340' side='right'caption='[[3i7v]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i7v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aquae Aquae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3I7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i7v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquae Aquae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i7u\|3i7u]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3i7u\|3i7u]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [~~http~~://pdbe.org/3i7v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3i7v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7v 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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [https://pdbe.org/3i7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [https://www.ebi.ac.uk/pdbsum/3i7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7v ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Aquae]]		[[Category: Aquae]]
		+	[[Category: Large Structures]]
	[[Category: Jeyakanthan, J]]		[[Category: Jeyakanthan, J]]
	[[Category: Kanaujia, S P]]		[[Category: Kanaujia, S P]]

OCA at 09:51, 19 December 2018

2018-12-19T09:51:36Z

←Older revision		Revision as of 09:51, 19 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5==		==Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5==
	<StructureSection load='3i7v' size='340' side='right' caption='[[3i7v]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3i7v' size='340' side='right' caption='[[3i7v]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i7u\|3i7u]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i7u\|3i7u]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [http://pdbe.org/3i7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [http://www.ebi.ac.uk/pdbsum/3i7v 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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [http://pdbe.org/3i7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [http://www.ebi.ac.uk/pdbsum/3i7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7v ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i7/3i7v_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i7/3i7v_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 23:46, 8 February 2016

2016-02-08T23:46:26Z

←Older revision		Revision as of 23:46, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3i7v' size='340' side='right' caption='[[3i7v]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3i7v' size='340' side='right' caption='[[3i7v]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i7v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aquifex_aeolicus_vf5 Aquifex aeolicus vf5~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i7v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i7u\|3i7u]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i7u\|3i7u]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 ~~Aquifex aeolicus VF5~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [http://www.ebi.ac.uk/pdbsum/3i7v 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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [http://pdbe.org/3i7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [http://www.ebi.ac.uk/pdbsum/3i7v PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=3i7v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 3i7v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aquifex aeolicus vf5~~]]	+	[[Category: Aquae]]
	[[Category: Jeyakanthan, J]]		[[Category: Jeyakanthan, J]]
	[[Category: Kanaujia, S P]]		[[Category: Kanaujia, S P]]

OCA at 06:09, 18 December 2014

2014-12-18T06:09:22Z

←Older revision		Revision as of 06:09, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3i7v\| PDB=3i7v \| SCENE= }}~~	+	==Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5==
-	===Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5===	+	<StructureSection load='3i7v' size='340' side='right' caption='[[3i7v]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20124691}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3i7v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7V FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i7u\|3i7u]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apfA, aq_158 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 Aquifex aeolicus VF5])</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=3i7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i7v RCSB], [http://www.ebi.ac.uk/pdbsum/3i7v 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/i7/3i7v_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 ==
		+	Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 A resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alphabetaalpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

-	~~==About this Structure==~~	+	Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5.,Jeyakanthan J, Kanaujia SP, Nishida Y, Nakagawa N, Praveen S, Shinkai A, Kuramitsu S, Yokoyama S, Sekar K Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):116-24. Epub 2010, Jan 22. PMID:20124691<ref>PMID:20124691</ref>
-	~~[[3i7v]] is a 2 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5~~ Aquifex aeolicus ~~vf5]~~. ~~This structure supersedes the now removed PDB entry [http~~:~~//oca~~.~~weizmann~~.~~ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	<~~ref group="xtra">PMID:020124691<~~/~~ref~~><~~references group="xtra"~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Aquifex aeolicus vf5]]		[[Category: Aquifex aeolicus vf5]]
-	[[Category: Jeyakanthan, J.]]	+	[[Category: Jeyakanthan, J]]
-	[[Category: Kanaujia, S P.]]	+	[[Category: Kanaujia, S P]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Nakagawa, N.]]	+	[[Category: Nakagawa, N]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sekar, K.]]	+	[[Category: Sekar, K]]
-	[[Category: Shinkai, A.]]	+	[[Category: Shinkai, A]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Ap4a]]		[[Category: Ap4a]]
	[[Category: Diadenosine polyphosphate]]		[[Category: Diadenosine polyphosphate]]
Line 23:		Line 45:
	[[Category: Nppsfa]]		[[Category: Nppsfa]]
	[[Category: Nudix protein]]		[[Category: Nudix protein]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA: Protected "3i7v" [edit=sysop:move=sysop]

2013-03-13T10:45:10Z

Protected "3i7v" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:45, 13 March 2013

OCA at 10:45, 13 March 2013

2013-03-13T10:45:08Z

←Older revision		Revision as of 10:45, 13 March 2013
Line 1:		Line 1:
-	{{Seed}}
-	[[Image:3i7v.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3i7v", 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_3i7v\| PDB=3i7v \| SCENE= }}		{{STRUCTURE_3i7v\| PDB=3i7v \| SCENE= }}
-
	===Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5===		===Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20124691}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20124691 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20124691}}		{{ABSTRACT_PUBMED_20124691}}

	==About this Structure==		==About this Structure==
-	~~3I7V~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA].	+	[[3i7v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20124691~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020124691</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus vf5]]		[[Category: Aquifex aeolicus vf5]]
	[[Category: Jeyakanthan, J.]]		[[Category: Jeyakanthan, J.]]
Line 42:		Line 26:
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 17 09:52:29 2010''

OCA at 07:52, 17 February 2010

2010-02-17T07:52:30Z

←Older revision		Revision as of 07:52, 17 February 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3i7v.~~jpg~~\|left\|200px]]	+	[[Image:3i7v.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5===		===Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20124691}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20124691 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20124691}}

	==About this Structure==		==About this Structure==
-	3I7V is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA].	+	3I7V is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20124691</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus vf5]]		[[Category: Aquifex aeolicus vf5]]
	[[Category: Jeyakanthan, J.]]		[[Category: Jeyakanthan, J.]]
Line 34:		Line 43:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 22 20~~:46:~~34 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 17 09:52:29 2010''

OCA at 17:46, 22 July 2009

2009-07-22T17:46:35Z

←Older revision		Revision as of 17:46, 22 July 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3i7v.jpg\|left\|200px]]

-	The ~~entry 3i7v~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3i7v", 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_3i7v\| PDB=3i7v \| SCENE= }}

-	~~Authors: Jeyakanthan, J., Kanaujia, S.P., Nakagawa, N., Sekar, K., Kuramitsu, S., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative~~ (~~RSGI~~)	+	===Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5===

-	Description: Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul ~~15 08~~:30:53 2009''	+	==About this Structure==
		+	3I7V is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pq1 2pq1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7V OCA].
		+	[[Category: Aquifex aeolicus vf5]]
		+	[[Category: Jeyakanthan, J.]]
		+	[[Category: Kanaujia, S P.]]
		+	[[Category: Kuramitsu, S.]]
		+	[[Category: Nakagawa, N.]]
		+	[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
		+	[[Category: Sekar, K.]]
		+	[[Category: Shinkai, A.]]
		+	[[Category: Yokoyama, S.]]
		+	[[Category: Ap4a]]
		+	[[Category: Diadenosine polyphosphate]]
		+	[[Category: Hydrolase]]
		+	[[Category: National project on protein structural and functional analyse]]
		+	[[Category: Nppsfa]]
		+	[[Category: Nudix protein]]
		+	[[Category: Riken structural genomics/proteomics initiative]]
		+	[[Category: Rsgi]]
		+	[[Category: Structural genomic]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 20:46:34 2009''

OCA: New page: '''Unreleased structure''' The entry 3i7v is ON HOLD Authors: Jeyakanthan, J., Kanaujia, S.P., Nakagawa, N., Sekar, K., Kuramitsu, S., Shinkai, A., Yokoyama, S., RIKEN Structural Genomi...

2009-07-15T05:30:53Z

New page: '''Unreleased structure''' The entry 3i7v is ON HOLD Authors: Jeyakanthan, J., Kanaujia, S.P., Nakagawa, N., Sekar, K., Kuramitsu, S., Shinkai, A., Yokoyama, S., RIKEN Structural Genomi...

New page

'''Unreleased structure'''

The entry 3i7v is ON HOLD

Authors: Jeyakanthan, J., Kanaujia, S.P., Nakagawa, N., Sekar, K., Kuramitsu, S., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Description: Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex aeolicus Vf5

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 15 08:30:53 2009''