1b99 - Revision history

OCA at 05:38, 9 August 2023

OCA — Wed, 09 Aug 2023 05:38:19 GMT

←Older revision		Revision as of 05:38, 9 August 2023
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	<StructureSection load='1b99' size='340' side='right'caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1b99' size='340' side='right'caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B99 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B99 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FUP:2,3~~-~~DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>~~, ~~<scene name='pdbligand=POP:PYROPHOSPHATE+~~2~~-'>POP</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]] 2.7Å</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=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [https://pdbe.org/1b99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [https://www.ebi.ac.uk/pdbsum/1b99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b99 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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [https://pdbe.org/1b99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [https://www.ebi.ac.uk/pdbsum/1b99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b99 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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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 11735~~]]	+	[[Category: Dictyostelium discoideum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Nucleoside-diphosphate kinase]]~~	+	[[Category: Janin J]]
-	[[Category: Janin, J]]	+	[[Category: Xu Y]]
-	[[Category: Xu, Y]]	+
-	~~[[Category: Antiviral agent]]~~	+
-	~~[[Category: Fluorouridine]]~~	+
-	~~[[Category: Phosphotransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 15:05, 2 June 2021

OCA — Wed, 02 Jun 2021 15:05:40 GMT

←Older revision		Revision as of 15:05, 2 June 2021
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	<StructureSection load='1b99' size='340' side='right'caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1b99' size='340' side='right'caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1B99 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B99 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [~~http~~://pdbe.org/1b99 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1b99 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1b99 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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [https://pdbe.org/1b99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [https://www.ebi.ac.uk/pdbsum/1b99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b99 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 29:		Line 29:

	==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 16:45, 28 August 2019

OCA — Wed, 28 Aug 2019 16:45:49 GMT

←Older revision		Revision as of 16:45, 28 August 2019
Line 1:		Line 1:

	==3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==		==3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==
-	<StructureSection load='1b99' size='340' side='right' caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='1b99' size='340' side='right'caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B99 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B99 FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b9/1b99_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b9/1b99_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 27:
	</div>		</div>
	<div class="pdbe-citations 1b99" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1b99" 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: Janin, J]]		[[Category: Janin, J]]

OCA at 11:11, 22 November 2017

OCA — Wed, 22 Nov 2017 11:11:25 GMT

←Older revision		Revision as of 11:11, 22 November 2017
Line 1:		Line 1:
		+
	==3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==		==3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==
	<StructureSection load='1b99' size='340' side='right' caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1b99' size='340' side='right' caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [http://pdbe.org/1b99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [http://www.ebi.ac.uk/pdbsum/1b99 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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [http://pdbe.org/1b99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [http://www.ebi.ac.uk/pdbsum/1b99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b99 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 1b99" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1b99" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:12, 10 February 2016

OCA — Wed, 10 Feb 2016 05:12:16 GMT

←Older revision		Revision as of 05:12, 10 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=1b99 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:42, 11 September 2015

OCA — Fri, 11 Sep 2015 05:42:31 GMT

←Older revision		Revision as of 05:42, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1b99' size='340' side='right' caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1b99' size='340' side='right' caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B99 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B99 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [http://www.ebi.ac.uk/pdbsum/1b99 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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [http://pdbe.org/1b99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [http://www.ebi.ac.uk/pdbsum/1b99 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 1b99" 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: Janin, J]]		[[Category: Janin, J]]

OCA at 10:06, 22 December 2014

OCA — Mon, 22 Dec 2014 10:06:52 GMT

←Older revision		Revision as of 10:06, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B99 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B99 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [http://www.ebi.ac.uk/pdbsum/1b99 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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [http://www.ebi.ac.uk/pdbsum/1b99 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: Janin, J.]]	+	[[Category: Janin, J]]
-	[[Category: Xu, Y.]]	+	[[Category: Xu, Y]]
	[[Category: Antiviral agent]]		[[Category: Antiviral agent]]
	[[Category: Fluorouridine]]		[[Category: Fluorouridine]]
	[[Category: Phosphotransferase]]		[[Category: Phosphotransferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 03:14, 7 August 2014

OCA — Thu, 07 Aug 2014 03:14:31 GMT

←Older revision		Revision as of 03:14, 7 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1b99.~~png\|left~~\|200px]]	+	==3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==
		+	<StructureSection load='1b99' size='340' side='right' caption='[[1b99]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1b99]] is a 6 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=1B99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B99 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUP:2,3-DIDEOXY-3-FLUORO-URIDIDINE-5-DIPHOSPHATE'>FUP</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=1b99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b99 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b99 RCSB], [http://www.ebi.ac.uk/pdbsum/1b99 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/b9/1b99_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 ==
		+	Nucleoside diphosphate (NDP) kinases display low specificity with respect to the base moiety of the nucleotides and to the 2'-position of the ribose, but the 3'-hydroxyl is found to be important for catalysis. We report in this paper the enzymatic analysis of a series of derivatives of thymidine diphosphate (TDP) where the 3'-OH group was removed or replaced by fluorine, azido, and amino groups. With Dictyostelium NDP kinase, kcat decreases 15-200-fold from 1100 s-1 with TDP, and (kcat/Km)NDP decreases from 12 x 10(6) to 10(3) to 5 x 10(4) M-1 s-1, depending on the substrate. The poorest substrates are 3'-deoxyTDP and 3'-azido-3'-deoxyTDP, while the best modified substrates are 2',3'-dehydro-3'-deoxyTDP and 3'-fluoro-3'-deoxyTDP. In a similar way, 3'-fluoro-2',3'-dideoxyUDP was found to be a better substrate than 2',3'-dideoxyUDP, but a much poorer substrate than 2'-deoxyUDP. (kcat/Km)NDP is sensitive to the viscosity of the solution with TDP as the substrate but not with the modified substrates. To understand the poor catalytic efficiency of the modified nucleotides at a structural level, we determined the crystal structure of Dictyostelium NDP kinase complexed to 3'-fluoro-2',3'-dideoxyUDP at 2.7 A resolution. Significant differences are noted as compared to the TDP complex. Substrate-assisted catalysis by the 3'-OH, which is effective in the NDP kinase reaction, cannot occur with the modified substrate. With TDP, the beta-phosphate, which is the leaving group when a gamma-phosphate is transferred to His122, hydrogen bonds to the 3'-hydroxyl group of the sugar; with 3'-fluoro-2',3'-dideoxyUDP, the beta-phosphate hydrogen bonds to Asn119 and moves away from the attacking Ndelta of the catalytic His122. Since all anti-AIDS nucleoside drugs are modified at the 3'-position, these results are relevant to the role of NDP kinase in their cellular metabolism.

-	~~{{STRUCTURE_1b99\| PDB=1b99 \| SCENE= }}~~	+	Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography.,Gonin P, Xu Y, Milon L, Dabernat S, Morr M, Kumar R, Lacombe ML, Janin J, Lascu I Biochemistry. 1999 Jun 1;38(22):7265-72. PMID:10353838<ref>PMID:10353838</ref>

-	~~===3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10353838}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1b99]] is~~ a ~~6 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=1B99 OCA].~~	+

	==See Also==		==See Also==
	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]		*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010353838<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]

OCA at 16:27, 20 October 2012

OCA — Sat, 20 Oct 2012 16:27:01 GMT

←Older revision		Revision as of 16:27, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1b99]] is a 6 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=1B99 OCA].	+	[[1b99]] is a 6 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=1B99 OCA].

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

OCA: Protected "1b99" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 21:43:34 GMT

Protected "1b99" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:43, 26 July 2012