1f3f - Revision history

OCA at 07:10, 7 February 2024

OCA — Wed, 07 Feb 2024 07:10:16 GMT

←Older revision		Revision as of 07:10, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='1f3f' size='340' side='right'caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1f3f' size='340' side='right'caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Dicdi Dicdi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F3F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F3F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.85Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [https://pdbe.org/1f3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [https://www.ebi.ac.uk/pdbsum/1f3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3f 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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [https://pdbe.org/1f3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [https://www.ebi.ac.uk/pdbsum/1f3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3f ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1f3f 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=1f3f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	AIDS chemotherapy is limited by inadequate intracellular concentrations of the active triphosphate form of nucleoside analogues, leading to incomplete inhibition of viral replication and the appearance of drug-resistant virus. Drug activation by nucleoside diphosphate kinase and inhibition of HIV-1 reverse transcriptase were studied comparatively. We synthesized analogues with a borano (BH(3)(-)) group on the alpha-phosphate, and found that they are substrates for both enzymes. X-ray structures of complexes with nucleotide diphosphate kinase provided a structural basis for their activation. The complex with d4T triphosphate displayed an intramolecular CH.O bond contributing to catalysis, and the R(p) diastereoisomer of thymidine alpha-boranotriphosphate bound like a normal substrate. Using alpha-(R(p))-boranophosphate derivatives of the clinically relevant compounds AZT and d4T, the presence of the alpha-borano group improved both phosphorylation by nucleotide diphosphate kinase and inhibition of reverse transcription. Moreover, repair of blocked DNA chains by pyrophosphorolysis was reduced significantly in variant reverse transcriptases bearing substitutions found in drug-resistant viruses. Thus, the alpha-borano modification of analogues targeting reverse transcriptase may be of generic value in fighting viral drug resistance.
-
-	Structural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase.,Meyer P, Schneider B, Sarfati S, Deville-Bonne D, Guerreiro C, Boretto J, Janin J, Veron M, Canard B EMBO J. 2000 Jul 17;19(14):3520-9. PMID:10899107<ref>PMID:10899107</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1f3f" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Nucleoside diphosphate kinase 3D structures\|Nucleoside diphosphate kinase 3D structures]]		*[[Nucleoside diphosphate kinase 3D structures\|Nucleoside diphosphate kinase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dicdi~~]]	+	[[Category: Dictyostelium discoideum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Nucleoside-diphosphate kinase]]~~	+	[[Category: Boretto J]]
-	[[Category: Boretto, J]]	+	[[Category: Canard B]]
-	[[Category: Canard, B]]	+	[[Category: Deville-Bonne D]]
-	[[Category: Deville-Bonne, D]]	+	[[Category: Guerreiro C]]
-	[[Category: Guerreiro, C]]	+	[[Category: Janin J]]
-	[[Category: Janin, J]]	+	[[Category: Meyer P]]
-	[[Category: Meyer, P]]	+	[[Category: Sarfati S]]
-	[[Category: Sarfati, S]]	+	[[Category: Schneider B]]
-	[[Category: Schneider, B]]	+	[[Category: Veron M]]
-	[[Category: Veron, M]]	+
-	~~[[Category: Anti-hiv nucleoside analogue]]~~	+
-	~~[[Category: Ch...o bond]]~~	+
-	~~[[Category: Nucleoside diphosphate kinase]]~~	+
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 15:09, 3 November 2021

OCA — Wed, 03 Nov 2021 15:09:01 GMT

←Older revision		Revision as of 15:09, 3 November 2021
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	<StructureSection load='1f3f' size='340' side='right'caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1f3f' size='340' side='right'caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_11735 Atcc 11735~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F3F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Dicdi Dicdi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F3F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 11735~~]]	+	[[Category: Dicdi]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]

OCA at 09:45, 21 July 2021

OCA — Wed, 21 Jul 2021 09:45:58 GMT

←Older revision		Revision as of 09:45, 21 July 2021
Line 3:		Line 3:
	<StructureSection load='1f3f' size='340' side='right'caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1f3f' size='340' side='right'caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1F3F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F3F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [~~http~~://pdbe.org/1f3f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1f3f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3f 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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [https://pdbe.org/1f3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [https://www.ebi.ac.uk/pdbsum/1f3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3f ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
-	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]	+	*[[Nucleoside diphosphate kinase 3D structures\|Nucleoside diphosphate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:30, 16 October 2019

OCA — Wed, 16 Oct 2019 11:30:05 GMT

←Older revision		Revision as of 11:30, 16 October 2019
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	==STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX==		==STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX==
-	<StructureSection load='1f3f' size='340' side='right' caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='1f3f' size='340' side='right'caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3F FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3F FirstGlance]. <br>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1f3f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1f3f" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 11735]]		[[Category: Atcc 11735]]
		+	[[Category: Large Structures]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Boretto, J]]		[[Category: Boretto, J]]

OCA at 09:36, 27 December 2017

OCA — Wed, 27 Dec 2017 09:36:24 GMT

←Older revision		Revision as of 09:36, 27 December 2017
Line 1:		Line 1:
		+
	==STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX==		==STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX==
	<StructureSection load='1f3f' size='340' side='right' caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1f3f' size='340' side='right' caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [http://pdbe.org/1f3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [http://www.ebi.ac.uk/pdbsum/1f3f 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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [http://pdbe.org/1f3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [http://www.ebi.ac.uk/pdbsum/1f3f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f3f ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/1f3f_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/1f3f_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 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1f3f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1f3f" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:13, 8 February 2016

OCA — Mon, 08 Feb 2016 20:13:29 GMT

←Older revision		Revision as of 20:13, 8 February 2016
Line 15:		Line 15:
	<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=1f3f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:00, 10 September 2015

OCA — Thu, 10 Sep 2015 15:00:22 GMT

←Older revision		Revision as of 15:00, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1f3f' size='340' side='right' caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='1f3f' size='340' side='right' caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Dictyostelium_discoideum Dictyostelium discoideum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [http://www.ebi.ac.uk/pdbsum/1f3f 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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [http://pdbe.org/1f3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [http://www.ebi.ac.uk/pdbsum/1f3f PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1f3f" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dictyostelium discoideum~~]]	+	[[Category: Atcc 11735]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Boretto, J]]		[[Category: Boretto, J]]

OCA at 23:41, 22 December 2014

OCA — Mon, 22 Dec 2014 23:41:29 GMT

←Older revision		Revision as of 23:41, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3F FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3F FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [http://www.ebi.ac.uk/pdbsum/1f3f 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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [http://www.ebi.ac.uk/pdbsum/1f3f 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 34:		Line 34:
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
-	[[Category: Boretto, J.]]	+	[[Category: Boretto, J]]
-	[[Category: Canard, B.]]	+	[[Category: Canard, B]]
-	[[Category: Deville-Bonne, D.]]	+	[[Category: Deville-Bonne, D]]
-	[[Category: Guerreiro, C.]]	+	[[Category: Guerreiro, C]]
-	[[Category: Janin, J.]]	+	[[Category: Janin, J]]
-	[[Category: Meyer, P.]]	+	[[Category: Meyer, P]]
-	[[Category: Sarfati, S.]]	+	[[Category: Sarfati, S]]
-	[[Category: Schneider, B.]]	+	[[Category: Schneider, B]]
-	[[Category: Veron, M.]]	+	[[Category: Veron, M]]
	[[Category: Anti-hiv nucleoside analogue]]		[[Category: Anti-hiv nucleoside analogue]]
	[[Category: Ch...o bond]]		[[Category: Ch...o bond]]

OCA at 13:25, 28 September 2014

OCA — Sun, 28 Sep 2014 13:25:10 GMT

←Older revision		Revision as of 13:25, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1f3f.~~png\|left~~\|200px]]	+	==STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX==
		+	<StructureSection load='1f3f' size='340' side='right' caption='[[1f3f]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1f3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F3F FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D4D:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-DIPHOSPHATE'>D4D</scene>, <scene name='pdbligand=D4T:2,3-DEHYDRO-2,3-DEOXY-THYMIDINE+5-TRIPHOSPHATE'>D4T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1f3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f3f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f3f RCSB], [http://www.ebi.ac.uk/pdbsum/1f3f 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/f3/1f3f_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 ==
		+	AIDS chemotherapy is limited by inadequate intracellular concentrations of the active triphosphate form of nucleoside analogues, leading to incomplete inhibition of viral replication and the appearance of drug-resistant virus. Drug activation by nucleoside diphosphate kinase and inhibition of HIV-1 reverse transcriptase were studied comparatively. We synthesized analogues with a borano (BH(3)(-)) group on the alpha-phosphate, and found that they are substrates for both enzymes. X-ray structures of complexes with nucleotide diphosphate kinase provided a structural basis for their activation. The complex with d4T triphosphate displayed an intramolecular CH.O bond contributing to catalysis, and the R(p) diastereoisomer of thymidine alpha-boranotriphosphate bound like a normal substrate. Using alpha-(R(p))-boranophosphate derivatives of the clinically relevant compounds AZT and d4T, the presence of the alpha-borano group improved both phosphorylation by nucleotide diphosphate kinase and inhibition of reverse transcription. Moreover, repair of blocked DNA chains by pyrophosphorolysis was reduced significantly in variant reverse transcriptases bearing substitutions found in drug-resistant viruses. Thus, the alpha-borano modification of analogues targeting reverse transcriptase may be of generic value in fighting viral drug resistance.

-	~~{{STRUCTURE_1f3f\| PDB=1f3f \| SCENE= }}~~	+	Structural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase.,Meyer P, Schneider B, Sarfati S, Deville-Bonne D, Guerreiro C, Boretto J, Janin J, Veron M, Canard B EMBO J. 2000 Jul 17;19(14):3520-9. PMID:10899107<ref>PMID:10899107</ref>

-	~~===STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE~~ / ~~D4T-TRIPHOSPHATE.MG COMPLEX===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10899107}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1f3f]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA].~~	+

	==See Also==		==See Also==
	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]		*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010899107<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]

OCA at 11:20, 20 October 2012

OCA — Sat, 20 Oct 2012 11:20:36 GMT

←Older revision		Revision as of 11:20, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1f3f]] is a 3 chain structure ~~of [[Nucleoside diphosphate kinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA].	+	[[1f3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F3F OCA].

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