1v8s - Revision history

OCA at 23:59, 27 December 2023

OCA — Wed, 27 Dec 2023 23:59:42 GMT

←Older revision		Revision as of 23:59, 27 December 2023
Line 3:		Line 3:
	<StructureSection load='1v8s' size='340' side='right'caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1v8s' size='340' side='right'caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V8S FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13]~~ </~~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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [https://pdbe.org/1v8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [https://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8s ProSAT], [https://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [https://pdbe.org/1v8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [https://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8s ProSAT], [https://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q84CU3_THETH Q84CU3_THETH]
	== 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: Flavobacterium thermophilum yoshida and oshima 1971]]
-	[[Category: ADP-ribose diphosphatase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Inoue, Y]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Kuramitsu, S]]	+	[[Category: Inoue Y]]
-	[[Category: Masui, R]]	+	[[Category: Kuramitsu S]]
-	[[Category: Nakagawa, N]]	+	[[Category: Masui R]]
-	[[Category: Ooga, T]]	+	[[Category: Nakagawa N]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Ooga T]]
-	[[Category: Shibata, T]]	+	[[Category: Shibata T]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	[[Category: Yoshiba, S]]	+	[[Category: Yoshiba S]]
-	~~[[Category: Helix-loop-helix]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mutt family]]~~	+
-	~~[[Category: Nudix motif]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 06:27, 6 October 2021

OCA — Wed, 06 Oct 2021 06:27:40 GMT

←Older revision		Revision as of 06:27, 6 October 2021
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	<StructureSection load='1v8s' size='340' side='right'caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1v8s' size='340' side='right'caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1V8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V8S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [~~http~~://pdbe.org/1v8s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8s ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [https://pdbe.org/1v8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [https://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8s ProSAT], [https://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 12:59, 1 January 2020

OCA — Wed, 01 Jan 2020 12:59:23 GMT

←Older revision		Revision as of 12:59, 1 January 2020
Line 1:		Line 1:

	==Crystal structure analusis of the ADP-ribose pyrophosphatase complexed with AMP and Mg==		==Crystal structure analusis of the ADP-ribose pyrophosphatase complexed with AMP and Mg==
-	<StructureSection load='1v8s' size='340' side='right' caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1v8s' size='340' side='right'caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V8S FirstGlance]. <br>		<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V8S FirstGlance]. <br>
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[ADP-ribose pyrophosphatase\|ADP-ribose pyrophosphatase]]	+	*[[ADP-ribose pyrophosphatase 3D structures\|ADP-ribose pyrophosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: ADP-ribose diphosphatase]]		[[Category: ADP-ribose diphosphatase]]
		+	[[Category: Large Structures]]
	[[Category: Inoue, Y]]		[[Category: Inoue, Y]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]

OCA at 07:48, 28 March 2018

OCA — Wed, 28 Mar 2018 07:48:33 GMT

←Older revision		Revision as of 07:48, 28 March 2018
Line 1:		Line 1:
		+
	==Crystal structure analusis of the ADP-ribose pyrophosphatase complexed with AMP and Mg==		==Crystal structure analusis of the ADP-ribose pyrophosphatase complexed with AMP and Mg==
	<StructureSection load='1v8s' size='340' side='right' caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1v8s' size='340' side='right' caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [http://pdbe.org/1v8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [http://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [http://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [http://pdbe.org/1v8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [http://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8s ProSAT], [http://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v8/1v8s_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v8/1v8s_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 16:35, 8 February 2016

OCA — Mon, 08 Feb 2016 16:35:49 GMT

←Older revision		Revision as of 16:35, 8 February 2016
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=1v8s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:27, 10 September 2015

OCA — Thu, 10 Sep 2015 13:27:34 GMT

←Older revision		Revision as of 13:27, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1v8s' size='340' side='right' caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1v8s' size='340' side='right' caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V8S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [http://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [http://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [http://pdbe.org/1v8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [http://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [http://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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 1v8s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: ADP-ribose diphosphatase]]		[[Category: ADP-ribose diphosphatase]]
-	[[Category: Thermus thermophilus]]
	[[Category: Inoue, Y]]		[[Category: Inoue, Y]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]

OCA at 12:37, 6 January 2015

OCA — Tue, 06 Jan 2015 12:37:28 GMT

←Older revision		Revision as of 12:37, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V8S FirstGlance]. <br>		<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V8S FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [http://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [http://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [http://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [http://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: ADP-ribose diphosphatase]]		[[Category: ADP-ribose diphosphatase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Inoue, Y.]]	+	[[Category: Inoue, Y]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Masui, R.]]	+	[[Category: Masui, R]]
-	[[Category: Nakagawa, N.]]	+	[[Category: Nakagawa, N]]
-	[[Category: Ooga, T.]]	+	[[Category: Ooga, T]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Shibata, T.]]	+	[[Category: Shibata, T]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
-	[[Category: Yoshiba, S.]]	+	[[Category: Yoshiba, S]]
	[[Category: Helix-loop-helix]]		[[Category: Helix-loop-helix]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Mutt family]]		[[Category: Mutt family]]
	[[Category: Nudix motif]]		[[Category: Nudix motif]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 22:21, 28 September 2014

OCA — Sun, 28 Sep 2014 22:21:05 GMT

←Older revision		Revision as of 22:21, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1v8s.~~png~~\|~~left~~\|200px]]	+	==Crystal structure analusis of the ADP-ribose pyrophosphatase complexed with AMP and Mg==
		+	<StructureSection load='1v8s' size='340' side='right' caption='[[1v8s]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1v8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V8S FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1v8i\|1v8i]], [[1v8l\|1v8l]], [[1v8m\|1v8m]], [[1v8n\|1v8n]], [[1v8r\|1v8r]], [[1v8t\|1v8t]], [[1v8u\|1v8u]], [[1v8v\|1v8v]], [[1v8w\|1v8w]], [[1v8y\|1v8y]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </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=1v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v8s RCSB], [http://www.ebi.ac.uk/pdbsum/1v8s PDBsum], [http://www.topsan.org/Proteins/RSGI/1v8s TOPSAN]</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/v8/1v8s_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 ==
		+	ADP-ribose pyrophosphatase (ADPRase) catalyzes the divalent metal ion-dependent hydrolysis of ADP-ribose to ribose 5'-phosphate and AMP. This enzyme plays a key role in regulating the intracellular ADP-ribose levels, and prevents nonenzymatic ADP-ribosylation. To elucidate the pyrophosphatase hydrolysis mechanism employed by this enzyme, structural changes occurring on binding of substrate, metal and product were investigated using crystal structures of ADPRase from an extreme thermophile, Thermus thermophilus HB8. Seven structures were determined, including that of the free enzyme, the Zn(2+)-bound enzyme, the binary complex with ADP-ribose, the ternary complexes with ADP-ribose and Zn(2+) or Gd(3+), and the product complexes with AMP and Mg(2+) or with ribose 5'-phosphate and Zn(2+). The structural and functional studies suggested that the ADP-ribose hydrolysis pathway consists of four reaction states: bound with metal (I), metal and substrate (II), metal and substrate in the transition state (III), and products (IV). In reaction state II, Glu-82 and Glu-70 abstract a proton from a water molecule. This water molecule is situated at an ideal position to carry out nucleophilic attack on the adenosyl phosphate, as it is 3.6 A away from the target phosphorus and almost in line with the scissile bond.

-	~~{{STRUCTURE_1v8s\| PDB=1v8s \| SCENE= }}~~	+	Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.,Yoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, Masui R J Biol Chem. 2004 Aug 27;279(35):37163-74. Epub 2004 Jun 21. PMID:15210687<ref>PMID:15210687</ref>

-	~~===Crystal structure analusis~~ of the ~~ADP-ribose pyrophosphatase complexed with AMP and Mg===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15210687}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1v8s]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA].~~	+

	==See Also==		==See Also==
	*[[ADP-ribose pyrophosphatase\|ADP-ribose pyrophosphatase]]		*[[ADP-ribose pyrophosphatase\|ADP-ribose pyrophosphatase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015210687<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: ADP-ribose diphosphatase]]		[[Category: ADP-ribose diphosphatase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 10:46, 20 October 2012

OCA — Sat, 20 Oct 2012 10:46:16 GMT

←Older revision		Revision as of 10:46, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1v8s]] is a 1 chain structure ~~of [[ADP-ribose pyrophosphatase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA].	+	[[1v8s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8S OCA].

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

OCA: Protected "1v8s" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 03:13:12 GMT

Protected "1v8s" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:13, 26 July 2012