1z4q - Revision history

OCA at 08:08, 15 May 2024

OCA — Wed, 15 May 2024 08:08:51 GMT

←Older revision		Revision as of 08:08, 15 May 2024
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	<StructureSection load='1z4q' size='340' side='right'caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1z4q' size='340' side='right'caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</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]] 2.05Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [https://pdbe.org/1z4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [https://www.ebi.ac.uk/pdbsum/1z4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z4q 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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [https://pdbe.org/1z4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [https://www.ebi.ac.uk/pdbsum/1z4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z4q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NT5M_HUMAN NT5M_HUMAN]] Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.	+	[https://www.uniprot.org/uniprot/NT5M_HUMAN NT5M_HUMAN] Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bianchi, V]]	+	[[Category: Bianchi V]]
-	[[Category: Nordlund, P]]	+	[[Category: Nordlund P]]
-	[[Category: Rinaldo-Matthis, A]]	+	[[Category: Rinaldo-Matthis A]]
-	[[Category: Ruzzenente, B]]	+	[[Category: Ruzzenente B]]
-	[[Category: Wallden, K]]	+	[[Category: Wallden K]]
-	~~[[Category: Alfa beta fold]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:43, 10 November 2021

OCA — Wed, 10 Nov 2021 06:43:08 GMT

←Older revision		Revision as of 06:43, 10 November 2021
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	<StructureSection load='1z4q' size='340' side='right'caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1z4q' size='340' side='right'caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</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=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</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">[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</div></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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [~~http~~://pdbe.org/1z4q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1z4q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1z4q 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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [https://pdbe.org/1z4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [https://www.ebi.ac.uk/pdbsum/1z4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z4q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NT5M_HUMAN NT5M_HUMAN]] Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.	+	[[https://www.uniprot.org/uniprot/NT5M_HUMAN NT5M_HUMAN]] Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:59, 5 February 2020

OCA — Wed, 05 Feb 2020 09:59:17 GMT

←Older revision		Revision as of 09:59, 5 February 2020
Line 1:		Line 1:

	==Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)==		==Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)==
-	<StructureSection load='1z4q' size='340' side='right' caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='1z4q' size='340' side='right'caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bianchi, V]]		[[Category: Bianchi, V]]
	[[Category: Nordlund, P]]		[[Category: Nordlund, P]]

OCA at 09:24, 2 May 2018

OCA — Wed, 02 May 2018 09:24:34 GMT

←Older revision		Revision as of 09:24, 2 May 2018
Line 1:		Line 1:
		+
	==Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)==		==Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)==
	<StructureSection load='1z4q' size='340' side='right' caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1z4q' size='340' side='right' caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</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=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</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">[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [http://pdbe.org/1z4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [http://www.ebi.ac.uk/pdbsum/1z4q 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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [http://pdbe.org/1z4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [http://www.ebi.ac.uk/pdbsum/1z4q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z4q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z4/1z4q_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z4/1z4q_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>
	</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=1z4q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:06, 11 September 2015

OCA — Fri, 11 Sep 2015 08:06:43 GMT

←Older revision		Revision as of 08:06, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1z4q' size='340' side='right' caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1z4q' size='340' side='right' caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</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=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</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">[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [http://www.ebi.ac.uk/pdbsum/1z4q 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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [http://pdbe.org/1z4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [http://www.ebi.ac.uk/pdbsum/1z4q PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1z4q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Bianchi, V]]		[[Category: Bianchi, V]]
	[[Category: Nordlund, P]]		[[Category: Nordlund, P]]

OCA at 13:38, 25 December 2014

OCA — Thu, 25 Dec 2014 13:38:44 GMT

←Older revision		Revision as of 13:38, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</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=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [http://www.ebi.ac.uk/pdbsum/1z4q 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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [http://www.ebi.ac.uk/pdbsum/1z4q PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NT5M_HUMAN NT5M_HUMAN]] Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Bianchi, V.]]	+	[[Category: Bianchi, V]]
-	[[Category: Nordlund, P.]]	+	[[Category: Nordlund, P]]
-	[[Category: Rinaldo-Matthis, A.]]	+	[[Category: Rinaldo-Matthis, A]]
-	[[Category: Ruzzenente, B.]]	+	[[Category: Ruzzenente, B]]
-	[[Category: Wallden, K.]]	+	[[Category: Wallden, K]]
	[[Category: Alfa beta fold]]		[[Category: Alfa beta fold]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 20:42, 29 September 2014

OCA — Mon, 29 Sep 2014 20:42:23 GMT

←Older revision		Revision as of 20:42, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1z4q.~~png~~\|~~left~~\|200px]]	+	==Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)==
		+	<StructureSection load='1z4q' size='340' side='right' caption='[[1z4q]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1z4q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z4Q FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4M:[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>D4M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z4i\|1z4i]], [[1z4j\|1z4j]], [[1z4k\|1z4k]], [[1z4l\|1z4l]], [[1z4m\|1z4m]], [[1z4p\|1z4p]]</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=1z4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z4q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1z4q RCSB], [http://www.ebi.ac.uk/pdbsum/1z4q 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/z4/1z4q_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 ==
		+	The human mitochondrial deoxyribonucleotidase catalyzes the dephosphorylation of thymidine and deoxyuridine monophosphates and participates in the regulation of the dTTP pool in mitochondria. We present seven structures of the inactive D41N variant of this enzyme in complex with thymidine 3'-monophosphate, thymidine 5'-monophosphate, deoxyuridine 5'-monophosphate, uridine 5'-monophosphate, deoxyguanosine 5'-monophosphate, uridine 2'-monophosphate, and the 5'-monophosphate of the nucleoside analog 3'-deoxy 2'3'-didehydrothymidine, and we draw conclusions about the substrate specificity based on comparisons with enzyme activities. We show that the enzyme's specificity for the deoxyribo form of nucleoside 5'-monophosphates is due to Ile-133, Phe-49, and Phe-102, which surround the 2' position of the sugar and cause an energetically unfavorable environment for the 2'-hydroxyl group of ribonucleoside 5'-monophosphates. The close binding of the 3'-hydroxyl group of nucleoside 5'-monophosphates to the enzyme indicates that nucleoside analog drugs that are substituted with a bulky group at this position will not be good substrates for this enzyme.

-	~~{{STRUCTURE_1z4q\| PDB=1z4q \| SCENE= }}~~	+	Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase.,Wallden K, Ruzzenente B, Rinaldo-Matthis A, Bianchi V, Nordlund P Structure. 2005 Jul;13(7):1081-8. PMID:16004879<ref>PMID:16004879</ref>

-	~~===Structure~~ of the ~~D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16004879}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1z4q]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016004879<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bianchi, V.]]		[[Category: Bianchi, V.]]

OCA: Protected "1z4q" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 17:49:23 GMT

Protected "1z4q" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:49, 5 January 2013

OCA at 17:49, 5 January 2013

OCA — Sat, 05 Jan 2013 17:49:20 GMT

←Older revision		Revision as of 17:49, 5 January 2013
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-	{{Seed}}
	[[Image:1z4q.png\|left\|200px]]		[[Image:1z4q.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1z4q", 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_1z4q\| PDB=1z4q \| SCENE= }}		{{STRUCTURE_1z4q\| PDB=1z4q \| SCENE= }}

	===Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)===		===Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16004879}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16004879 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16004879}}		{{ABSTRACT_PUBMED_16004879}}

	==About this Structure==		==About this Structure==
-	~~1Z4Q~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA].	+	[[1z4q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16004879~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016004879</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bianchi, V.]]		[[Category: Bianchi, V.]]
Line 31:		Line 19:
	[[Category: Wallden, K.]]		[[Category: Wallden, K.]]
	[[Category: Alfa beta fold]]		[[Category: Alfa beta fold]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 17:37:57 2009''~~	+

OCA at 15:38, 17 February 2009

OCA — Tue, 17 Feb 2009 15:38:00 GMT

←Older revision		Revision as of 15:38, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1Z4Q is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA].	+	1Z4Q is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z4Q OCA].

	==Reference==		==Reference==
-	~~Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase., Wallden K, Ruzzenente B, Rinaldo-Matthis A, Bianchi V, Nordlund P, Structure. 2005 Jul;13(7):1081-8.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16004879 16004879]~~	+	<ref group="xtra">PMID:16004879</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Single protein]]
	[[Category: Bianchi, V.]]		[[Category: Bianchi, V.]]
	[[Category: Nordlund, P.]]		[[Category: Nordlund, P.]]
Line 33:		Line 32:
	[[Category: Alfa beta fold]]		[[Category: Alfa beta fold]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 00~~:38:~~53 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:37:57 2009''