2pgr - Revision history

OCA at 11:01, 30 August 2023

2023-08-30T11:01:34Z

←Older revision		Revision as of 11:01, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2pgr' size='340' side='right'caption='[[2pgr]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2pgr' size='340' side='right'caption='[[2pgr]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pgr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Plavi Plavi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pgr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PGR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>~~, ~~<scene name='pdbligand=DCF:~~2~~-DEOXYCOFORMYCIN'>DCF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=DCF:2-DEOXYCOFORMYCIN'>DCF</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[2qvn\|2qvn]], [[2pgf\|2pgf]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class="sblockDat">Pv111245 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 PLAVI])</td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4]~~ </~~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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [https://pdbe.org/2pgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [https://www.ebi.ac.uk/pdbsum/2pgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgr 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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [https://pdbe.org/2pgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [https://www.ebi.ac.uk/pdbsum/2pgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgr ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ADA_PLAVS ADA_PLAVS] Catalyzes the hydrolytic deamination of adenosine to produce inosine (PubMed:19728741). Unlike mammalian adenosine deaminases, also catalyzes the deamination of 5'-methylthioadenosine (MTA), a by-product of polyamine biosynthesis, to produce 5'-methylthioinosine (MTI) (PubMed:19728741). Plays an essential role in the purine salvage pathway which allows the parasite to use host cell purines for the synthesis of nucleic acids (PubMed:19728741).<ref>PMID:19728741</ref>
	== 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: Adenosine deaminase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Plavi~~]]	+	[[Category: Plasmodium vivax]]
-	[[Category: Larson~~, E T~~]]	+	[[Category: Larson ET]]
-	[[Category: Merritt~~, E A]]~~	+	[[Category: Merritt EA]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metallo-dependent hydrolase]]~~	+
-	~~[[Category: Msgpp]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Sgpp~~]]	+

OCA at 15:23, 17 June 2021

2021-06-17T15:23:47Z

←Older revision		Revision as of 15:23, 17 June 2021
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	==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin==		==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin==
-	<StructureSection load='2pgr' size='340' side='right' caption='[[2pgr]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='2pgr' size='340' side='right'caption='[[2pgr]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pgr]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Plavi Plavi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pgr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Plavi Plavi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PGR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=DCF:2-DEOXYCOFORMYCIN'>DCF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=DCF:2-DEOXYCOFORMYCIN'>DCF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qvn\|2qvn]], [[2pgf\|2pgf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qvn\|2qvn]], [[2pgf\|2pgf]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pv111245 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 PLAVI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pv111245 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 PLAVI])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [~~http~~://pdbe.org/2pgr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pgr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgr 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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [https://pdbe.org/2pgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [https://www.ebi.ac.uk/pdbsum/2pgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pgr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pgr_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2pgr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2pgr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenosine deaminase 3D structures\|Adenosine deaminase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Adenosine deaminase]]		[[Category: Adenosine deaminase]]
		+	[[Category: Large Structures]]
	[[Category: Plavi]]		[[Category: Plavi]]
	[[Category: Larson, E T]]		[[Category: Larson, E T]]

OCA at 09:25, 18 October 2017

2017-10-18T09:25:14Z

←Older revision		Revision as of 09:25, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin==		==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin==
	<StructureSection load='2pgr' size='340' side='right' caption='[[2pgr]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2pgr' size='340' side='right' caption='[[2pgr]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pv111245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 PLAVI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pv111245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 PLAVI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [http://pdbe.org/2pgr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [http://www.ebi.ac.uk/pdbsum/2pgr 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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [http://pdbe.org/2pgr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [http://www.ebi.ac.uk/pdbsum/2pgr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 18:		Line 19:
	<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=2pgr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2pgr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2pgr" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Adenosine deaminase\|Adenosine deaminase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:49, 12 September 2015

2015-09-12T01:49:24Z

←Older revision		Revision as of 01:49, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2pgr' size='340' side='right' caption='[[2pgr]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2pgr' size='340' side='right' caption='[[2pgr]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pgr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Plasmodium_vivax Plasmodium vivax~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pgr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Plavi Plavi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=DCF:2-DEOXYCOFORMYCIN'>DCF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=DCF:2-DEOXYCOFORMYCIN'>DCF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qvn\|2qvn]], [[2pgf\|2pgf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qvn\|2qvn]], [[2pgf\|2pgf]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pv111245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 ~~Plasmodium vivax~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pv111245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 PLAVI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [http://www.ebi.ac.uk/pdbsum/2pgr 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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [http://pdbe.org/2pgr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [http://www.ebi.ac.uk/pdbsum/2pgr PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2pgr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Adenosine deaminase]]		[[Category: Adenosine deaminase]]
-	[[Category: ~~Plasmodium vivax~~]]	+	[[Category: Plavi]]
	[[Category: Larson, E T]]		[[Category: Larson, E T]]
	[[Category: Merritt, E A]]		[[Category: Merritt, E A]]

OCA at 17:01, 19 January 2015

2015-01-19T17:01:38Z

←Older revision		Revision as of 17:01, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pgr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pgr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=DCF:2-DEOXYCOFORMYCIN'>DCF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=DCF:2-DEOXYCOFORMYCIN'>DCF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qvn\|2qvn]], [[2pgf\|2pgf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qvn\|2qvn]], [[2pgf\|2pgf]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pv111245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 Plasmodium vivax])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pv111245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 Plasmodium vivax])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [http://www.ebi.ac.uk/pdbsum/2pgr 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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [http://www.ebi.ac.uk/pdbsum/2pgr PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	[[Category: Adenosine deaminase]]		[[Category: Adenosine deaminase]]
	[[Category: Plasmodium vivax]]		[[Category: Plasmodium vivax]]
-	[[Category: Larson, E T.]]	+	[[Category: Larson, E T]]
-	[[Category: Merritt, E A.]]	+	[[Category: Merritt, E A]]
-	[[Category: ~~SGPP,~~ Structural ~~Genomics of Pathogenic Protozoa Consortium.~~]]	+	[[Category: Structural genomic]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	[[Category: Medical structural genomics of pathogenic protozoa consortium]]
	[[Category: Metallo-dependent hydrolase]]		[[Category: Metallo-dependent hydrolase]]
	[[Category: Msgpp]]		[[Category: Msgpp]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi~~]]	+
	[[Category: Sgpp]]		[[Category: Sgpp]]
-	[[Category: Structural genomic]]
-	[[Category: Structural genomics of pathogenic protozoa consortium]]

OCA at 19:36, 30 September 2014

2014-09-30T19:36:20Z

←Older revision		Revision as of 19:36, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2pgr.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin==
		+	<StructureSection load='2pgr' size='340' side='right' caption='[[2pgr]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pgr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=DCF:2-DEOXYCOFORMYCIN'>DCF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qvn\|2qvn]], [[2pgf\|2pgf]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pv111245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 Plasmodium vivax])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </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=2pgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pgr RCSB], [http://www.ebi.ac.uk/pdbsum/2pgr 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/pg/2pgr_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 ==
		+	Plasmodium and other apicomplexan parasites are deficient in purine biosynthesis, relying instead on the salvage of purines from their host environment. Therefore, interference with the purine salvage pathway is an attractive therapeutic target. The plasmodial enzyme adenosine deaminase (ADA) plays a central role in purine salvage and, unlike mammalian ADA homologs, has a further secondary role in methylthiopurine recycling. For this reason, plasmodial ADA accepts a wider range of substrates, as it is responsible for deamination of both adenosine and 5'-methylthioadenosine. The latter substrate is not accepted by mammalian ADA homologs. The structural basis for this natural difference in specificity between plasmodial and mammalian ADA has not been well understood. We now report crystal structures of Plasmodium vivax ADA in complex with adenosine, guanosine, and the picomolar inhibitor 2'-deoxycoformycin. These structures highlight a drastic conformational change in plasmodial ADA upon substrate binding that has not been observed for mammalian ADA enzymes. Further, these complexes illuminate the structural basis for the differential substrate specificity and potential drug selectivity between mammalian and parasite enzymes.

-	~~{{STRUCTURE_2pgr\| PDB=2pgr \| SCENE= }}~~	+	Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity.,Larson ET, Deng W, Krumm BE, Napuli A, Mueller N, Van Voorhis WC, Buckner FS, Fan E, Lauricella A, DeTitta G, Luft J, Zucker F, Hol WG, Verlinde CL, Merritt EA J Mol Biol. 2008 Sep 12;381(4):975-88. Epub 2008 Jun 24. PMID:18602399<ref>PMID:18602399</ref>

-	~~===Crystal structure~~ of ~~adenosine deaminase from Plasmodium vivax in complex with pentostatin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_18602399}}~~	+	==See Also==
-		+	*[[Adenosine deaminase\|Adenosine deaminase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2pgr~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:018602399<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Adenosine deaminase]]		[[Category: Adenosine deaminase]]
	[[Category: Plasmodium vivax]]		[[Category: Plasmodium vivax]]

OCA: Protected "2pgr" [edit=sysop:move=sysop]

2013-01-07T14:37:44Z

Protected "2pgr" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:37, 7 January 2013

OCA at 14:37, 7 January 2013

2013-01-07T14:37:38Z

←Older revision		Revision as of 14:37, 7 January 2013
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-	{{Seed}}
	[[Image:2pgr.png\|left\|200px]]		[[Image:2pgr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2pgr", 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_2pgr\| PDB=2pgr \| SCENE= }}		{{STRUCTURE_2pgr\| PDB=2pgr \| SCENE= }}

	===Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin===		===Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18602399}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18602399 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18602399}}		{{ABSTRACT_PUBMED_18602399}}

	==About this Structure==		==About this Structure==
-	~~2PGR~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA].	+	[[2pgr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18602399~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018602399</ref><references group="xtra"/>
	[[Category: Adenosine deaminase]]		[[Category: Adenosine deaminase]]
	[[Category: Plasmodium vivax]]		[[Category: Plasmodium vivax]]
Line 29:		Line 17:
	[[Category: Merritt, E A.]]		[[Category: Merritt, E A.]]
	[[Category: SGPP, Structural Genomics of Pathogenic Protozoa Consortium.]]		[[Category: SGPP, Structural Genomics of Pathogenic Protozoa Consortium.]]
		+	[[Category: Hydrolase]]
	[[Category: Medical structural genomics of pathogenic protozoa consortium]]		[[Category: Medical structural genomics of pathogenic protozoa consortium]]
	[[Category: Metallo-dependent hydrolase]]		[[Category: Metallo-dependent hydrolase]]
Line 37:		Line 26:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Structural genomics of pathogenic protozoa consortium]]		[[Category: Structural genomics of pathogenic protozoa consortium]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:29:43 2009''

OCA at 07:29, 18 February 2009

2009-02-18T07:29:44Z

←Older revision		Revision as of 07:29, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA].	+	2PGR is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA].

	==Reference==		==Reference==
-	Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity., Larson ET, Deng W, Krumm BE, Napuli A, Mueller N, Van Voorhis WC, Buckner FS, Fan E, Lauricella A, DeTitta G, Luft J, Zucker F, Hol WG, Verlinde CL, Merritt EA, J Mol Biol. 2008 Sep 12;381(4):975-88. Epub 2008 Jun 24. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18602399 18602399]~~	+	<ref group="xtra">PMID:18602399</ref><references group="xtra"/>
	[[Category: Adenosine deaminase]]		[[Category: Adenosine deaminase]]
		+	[[Category: Plasmodium vivax]]
	[[Category: Larson, E T.]]		[[Category: Larson, E T.]]
	[[Category: Merritt, E A.]]		[[Category: Merritt, E A.]]
Line 37:		Line 38:
	[[Category: Structural genomics of pathogenic protozoa consortium]]		[[Category: Structural genomics of pathogenic protozoa consortium]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Aug 20 11~~:25:~~42 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:29:43 2009''

OCA at 08:25, 20 August 2008

2008-08-20T08:25:42Z

←Older revision		Revision as of 08:25, 20 August 2008
Line 1:		Line 1:
-	[[Image:2pgr.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2pgr.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2pgr\| PDB=2pgr \| SCENE= }}		{{STRUCTURE_2pgr\| PDB=2pgr \| SCENE= }}

-	~~'''~~Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin~~'''~~	+	===Crystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18602399}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18602399 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18602399}}

	==About this Structure==		==About this Structure==
	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA].		Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGR OCA].
		+
		+	==Reference==
		+	Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity., Larson ET, Deng W, Krumm BE, Napuli A, Mueller N, Van Voorhis WC, Buckner FS, Fan E, Lauricella A, DeTitta G, Luft J, Zucker F, Hol WG, Verlinde CL, Merritt EA, J Mol Biol. 2008 Sep 12;381(4):975-88. Epub 2008 Jun 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18602399 18602399]
	[[Category: Adenosine deaminase]]		[[Category: Adenosine deaminase]]
	[[Category: Larson, E T.]]		[[Category: Larson, E T.]]
Line 26:		Line 36:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Structural genomics of pathogenic protozoa consortium]]		[[Category: Structural genomics of pathogenic protozoa consortium]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 13~~:04:39 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 20 11:25:42 2008''