2pgf - Revision history

OCA at 05:25, 17 October 2024

2024-10-17T05:25:47Z

← Older revision		Revision as of 05:25, 17 October 2024
Line 15:		Line 15:
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pgf_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pgf_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 11:01, 30 August 2023

2023-08-30T11:01:24Z

← Older revision		Revision as of 11:01, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2pgf' size='340' side='right'caption='[[2pgf]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='2pgf' size='340' side='right'caption='[[2pgf]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pgf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Haemamoeba_vivax Haemamoeba~~ vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PGF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pgf]] 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=2PGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PGF FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>~~, ~~<scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.89Å</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=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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]]~~, ~~[[2pgr\|2pgr]]~~<~~/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 Haemamoeba vivax])</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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [https://pdbe.org/2pgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [https://www.ebi.ac.uk/pdbsum/2pgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgf 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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [https://pdbe.org/2pgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [https://www.ebi.ac.uk/pdbsum/2pgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgf 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]]
Line 38:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Adenosine deaminase]]~~
	~~[[Category: Haemamoeba vivax]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Larson, E T~~]]		[[Category: Plasmodium vivax]]
	[[Category: ~~Merritt, E A~~]]		[[Category: Larson ET]]
	[[Category: ~~Structural genomic]]~~		[[Category: Merritt EA]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: Metallo-dependent hydrolase]]~~
	~~[[Category: Msgpp]]~~
	~~[[Category: PSI, Protein structure initiative]]~~
	~~[[Category: Sgpp~~]]

OCA at 15:23, 17 June 2021

2021-06-17T15:23:34Z

← Older revision		Revision as of 15:23, 17 June 2021
Line 1:		Line 1:

	==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with adenosine==		==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with adenosine==
	<StructureSection load='2pgf' size='340' side='right' caption='[[2pgf]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='2pgf' size='340' side='right'caption='[[2pgf]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pgf]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Haemamoeba_vivax Haemamoeba vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PGF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pgf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemamoeba_vivax Haemamoeba vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PGF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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]], [[2pgr\|2pgr]]</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]], [[2pgr\|2pgr]]</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 Haemamoeba vivax])</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 Haemamoeba vivax])</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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [~~http~~://pdbe.org/2pgf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pgf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgf 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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [https://pdbe.org/2pgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [https://www.ebi.ac.uk/pdbsum/2pgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	==See Also==		==See Also==
	*[[Adenosine deaminase\|Adenosine deaminase]]		*[[Adenosine deaminase\|Adenosine deaminase]]
			*[[Adenosine deaminase 3D structures\|Adenosine deaminase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 40:
	[[Category: Adenosine deaminase]]		[[Category: Adenosine deaminase]]
	[[Category: Haemamoeba vivax]]		[[Category: Haemamoeba vivax]]
			[[Category: Large Structures]]
	[[Category: Larson, E T]]		[[Category: Larson, E T]]
	[[Category: Merritt, E A]]		[[Category: Merritt, E A]]

OCA at 08:54, 29 August 2018

2018-08-29T08:54:24Z

← Older revision		Revision as of 08:54, 29 August 2018
Line 1:		Line 1:

	==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with adenosine==		==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with adenosine==
	<StructureSection load='2pgf' size='340' side='right' caption='[[2pgf]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='2pgf' size='340' side='right' caption='[[2pgf]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pgf]] 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=2PGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pgf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemamoeba_vivax Haemamoeba vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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]], [[2pgr\|2pgr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qvn\|2qvn]], [[2pgr\|2pgr]]</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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5855 Haemamoeba vivax])</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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [http://pdbe.org/2pgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [http://www.ebi.ac.uk/pdbsum/2pgf 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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [http://pdbe.org/2pgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [http://www.ebi.ac.uk/pdbsum/2pgf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pgf_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pgf_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 37:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Adenosine deaminase]]		[[Category: Adenosine deaminase]]
	[[Category: ~~Plavi~~]]		[[Category: Haemamoeba vivax]]
	[[Category: Larson, E T]]		[[Category: Larson, E T]]
	[[Category: Merritt, E A]]		[[Category: Merritt, E A]]

OCA at 06:41, 8 February 2016

2016-02-08T06:41:00Z

← Older revision		Revision as of 06:41, 8 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pgf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:53, 10 September 2015

2015-09-10T08:53:44Z

← Older revision		Revision as of 08:53, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2pgf' size='340' side='right' caption='[[2pgf]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='2pgf' size='340' side='right' caption='[[2pgf]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pgf]] 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=2PGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pgf]] 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=2PGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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]], [[2pgr\|2pgr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qvn\|2qvn]], [[2pgr\|2pgr]]</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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [http://www.ebi.ac.uk/pdbsum/2pgf 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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [http://pdbe.org/2pgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [http://www.ebi.ac.uk/pdbsum/2pgf PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2pgf" 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 17:03, 19 January 2015

2015-01-19T17:03:55Z

← Older revision		Revision as of 17:03, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pgf]] 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=2PGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pgf]] 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=2PGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGF FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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]], [[2pgr\|2pgr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qvn\|2qvn]], [[2pgr\|2pgr]]</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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [http://www.ebi.ac.uk/pdbsum/2pgf 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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [http://www.ebi.ac.uk/pdbsum/2pgf 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 19:37, 30 September 2014

2014-09-30T19:37:42Z

← Older revision		Revision as of 19:37, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2pgf~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of adenosine deaminase from Plasmodium vivax in complex with adenosine==
			<StructureSection load='2pgf' size='340' side='right' caption='[[2pgf]], [[Resolution\|resolution]] 1.89Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2pgf]] 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=2PGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PGF FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</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]], [[2pgr\|2pgr]]</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=2pgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pgf RCSB], [http://www.ebi.ac.uk/pdbsum/2pgf 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/2pgf_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_2pgf\| PDB=2pgf \| 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 adenosine===~~		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 ==
	[[~~2pgf]] 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=2PGF 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 "2pgf" [edit=sysop:move=sysop]

2013-01-07T14:39:22Z

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

← Older revision	Revision as of 14:39, 7 January 2013
(No difference)

OCA at 14:39, 7 January 2013

2013-01-07T14:39:19Z

← Older revision		Revision as of 14:39, 7 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2pgf.png\|left\|200px]]		[[Image:2pgf.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2pgf", 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_2pgf\| PDB=2pgf \| SCENE= }}		{{STRUCTURE_2pgf\| PDB=2pgf \| SCENE= }}

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


	~~<!--~~
	~~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==
	~~2PGF~~ 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=2PGF OCA].		[[2pgf]] 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=2PGF 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 Mon Feb 16 19:52:47 2009''~~