1f6t - Revision history

OCA at 07:11, 7 February 2024

2024-02-07T07:11:30Z

←Older revision		Revision as of 07:11, 7 February 2024
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	<StructureSection load='1f6t' size='340' side='right'caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='1f6t' size='340' side='right'caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F6T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=TBD:2-DEOXY-THYMIDINE-5-ALPHA+BORANO+DIPHOSPHATE+(ISOMER+RP)'>TBD</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]] 1.92Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1f3f\|1f3f]], [[1lwx\|1lwx]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TBD:2-DEOXY-THYMIDINE-5-ALPHA+BORANO+DIPHOSPHATE+(ISOMER+RP)'>TBD</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [https://pdbe.org/1f6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [https://www.ebi.ac.uk/pdbsum/1f6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6t 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=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [https://pdbe.org/1f6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [https://www.ebi.ac.uk/pdbsum/1f6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6t 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=1f6t 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=1f6t 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 1f6t" 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: ~~Atcc 11735~~]]	+	[[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: Sarfati S]]
-	[[Category: Sarfati, S]]	+	[[Category: Schneider B]]
-	[[Category: Schneider, B]]	+	[[Category: Veron M]]
-	[[Category: Veron, M]]	+
-	~~[[Category: Anti-hiv nucleoside analogue]]~~	+
-	~~[[Category: Boranophosphate]]~~	+
-	~~[[Category: Nucleoside diphosphate kinase]]~~	+
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:47, 21 July 2021

2021-07-21T09:47:00Z

←Older revision		Revision as of 09:47, 21 July 2021
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	<StructureSection load='1f6t' size='340' side='right'caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='1f6t' size='340' side='right'caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1F6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F6T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TBD:2-DEOXY-THYMIDINE-5-ALPHA+BORANO+DIPHOSPHATE+(ISOMER+RP)'>TBD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TBD:2-DEOXY-THYMIDINE-5-ALPHA+BORANO+DIPHOSPHATE+(ISOMER+RP)'>TBD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f3f\|1f3f]], [[1lwx\|1lwx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f3f\|1f3f]], [[1lwx\|1lwx]]</div></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=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [~~http~~://pdbe.org/1f6t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1f6t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6t 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=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [https://pdbe.org/1f6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [https://www.ebi.ac.uk/pdbsum/1f6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6t ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==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 10:43, 16 October 2019

2019-10-16T10:43:01Z

←Older revision		Revision as of 10:43, 16 October 2019
Line 1:		Line 1:

	==STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX==		==STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX==
-	<StructureSection load='1f6t' size='340' side='right' caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>	+	<StructureSection load='1f6t' size='340' side='right'caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F6T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F6T FirstGlance]. <br>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1f6t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1f6t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	</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 09:29, 27 December 2017

2017-12-27T09:29:37Z

←Older revision		Revision as of 09:29, 27 December 2017
Line 1:		Line 1:
		+
	==STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX==		==STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX==
	<StructureSection load='1f6t' size='340' side='right' caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='1f6t' size='340' side='right' caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f3f\|1f3f]], [[1lwx\|1lwx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f3f\|1f3f]], [[1lwx\|1lwx]]</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=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [http://pdbe.org/1f6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [http://www.ebi.ac.uk/pdbsum/1f6t 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=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [http://pdbe.org/1f6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [http://www.ebi.ac.uk/pdbsum/1f6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6t ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/1f6t_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/1f6t_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 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1f6t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1f6t" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:20, 7 February 2016

2016-02-07T02:20:03Z

←Older revision		Revision as of 02:20, 7 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1f6t ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:44, 9 September 2015

2015-09-09T20:44:59Z

←Older revision		Revision as of 20:44, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1f6t' size='340' side='right' caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='1f6t' size='340' side='right' caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F6T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TBD:2-DEOXY-THYMIDINE-5-ALPHA+BORANO+DIPHOSPHATE+(ISOMER+RP)'>TBD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TBD:2-DEOXY-THYMIDINE-5-ALPHA+BORANO+DIPHOSPHATE+(ISOMER+RP)'>TBD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f3f\|1f3f]], [[1lwx\|1lwx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f3f\|1f3f]], [[1lwx\|1lwx]]</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=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [http://www.ebi.ac.uk/pdbsum/1f6t 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=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [http://pdbe.org/1f6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [http://www.ebi.ac.uk/pdbsum/1f6t PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1f6t" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__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 18:28, 22 December 2014

2014-12-22T18:28:36Z

←Older revision		Revision as of 18:28, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F6T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F6T FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TBD:2-DEOXY-THYMIDINE-5-ALPHA+BORANO+DIPHOSPHATE+(ISOMER+RP)'>TBD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TBD:2-DEOXY-THYMIDINE-5-ALPHA+BORANO+DIPHOSPHATE+(ISOMER+RP)'>TBD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f3f\|1f3f]], [[1lwx\|1lwx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f3f\|1f3f]], [[1lwx\|1lwx]]</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=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [http://www.ebi.ac.uk/pdbsum/1f6t 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=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [http://www.ebi.ac.uk/pdbsum/1f6t 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 35:		Line 35:
	[[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: 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: Boranophosphate]]		[[Category: Boranophosphate]]

OCA at 08:32, 28 September 2014

2014-09-28T08:32:14Z

←Older revision		Revision as of 08:32, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1f6t.~~png~~\|~~left~~\|200px]]	+	==STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX==
		+	<StructureSection load='1f6t' size='340' side='right' caption='[[1f6t]], [[Resolution\|resolution]] 1.92Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1f6t]] 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=1F6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F6T FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TBD:2-DEOXY-THYMIDINE-5-ALPHA+BORANO+DIPHOSPHATE+(ISOMER+RP)'>TBD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1f3f\|1f3f]], [[1lwx\|1lwx]]</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f6t RCSB], [http://www.ebi.ac.uk/pdbsum/1f6t 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/f6/1f6t_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_1f6t\| PDB=1f6t \| 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 NUCLEOSIDE DIPHOSPHATE KINASE~~/~~ALPHA-BORANO(RP)-TDP.MG COMPLEX===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10899107}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1f6t]] 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=1F6T 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 05:19, 20 October 2012

2012-10-20T05:19:37Z

←Older revision		Revision as of 05:19, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1f6t]] 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=1F6T OCA].	+	[[1f6t]] 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=1F6T OCA].

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

OCA: Protected "1f6t" [edit=sysop:move=sysop]

2012-07-25T09:41:02Z

Protected "1f6t" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:41, 25 July 2012