1nhk - Revision history

OCA at 07:56, 14 February 2024

2024-02-14T07:56:31Z

←Older revision		Revision as of 07:56, 14 February 2024
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	<StructureSection load='1nhk' size='340' side='right'caption='[[1nhk]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1nhk' size='340' side='right'caption='[[1nhk]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nhk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_25232 Atcc 25232~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1NHK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nhk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NHK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CMP:ADENOSINE~~-3,~~5-CYCLIC-MONOPHOSPHATE'>CMP</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]] 1.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=34 ATCC 25232])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [https://pdbe.org/1nhk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [https://www.ebi.ac.uk/pdbsum/1nhk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nhk ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [~~http~~://pdbe.org/1nhk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nhk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nhk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NDK_MYXXA NDK_MYXXA]] Major role in the synthesis of nucleoside triphosphates other than ATP.[HAMAP-Rule:MF_00451]	+	[https://www.uniprot.org/uniprot/NDK_MYXXA NDK_MYXXA] Major role in the synthesis of nucleoside triphosphates other than ATP.[HAMAP-Rule:MF_00451]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=1nhk 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=1nhk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The X-ray structure of Myxococcus xanthus nucleoside diphosphate (NDP) kinase complexed with adenosine 3',5'-cyclic monophosphate (cAMP) has been determined. The structure was solved by difference Fourier analysis. The refined structure has a crystallographic R-factor of 0.17 at 1.9 A resolution. The phosphoryl group and ribose moiety make extensive polar interactions with the protein, whereas the base interacts only with two hydrophobic residues. The comparison with the structure of the enzyme complex with the substrate adenosine diphosphate (ADP) reported earlier shows that cAMP and ADP interact similarly with the enzyme. The base of the cAMP is present in two conformations, syn and anti, with respect to the sugar. The syn conformer is dominant. Based on the effect of cAMP on phosphorylation of the human NDP kinase NM23, it had been proposed that cAMP might interact with NDP kinase in a manner distinct from other nucleotides. However, the structure of the M. xanthus NDP kinase/cAMP complex indicates that the nucleotide is a competitive inhibitor of the enzyme and occupies the usual nucleotide site. Kinetic assays of the NDP kinase activity in the presence of cAMP were done. Their results are consistent with a competitive character of the cAMP inhibition.
-
-	The 1.9 A crystal structure of a nucleoside diphosphate kinase complex with adenosine 3',5'-cyclic monophosphate: evidence for competitive inhibition.,Strelkov SV, Perisic O, Webb PA, Williams RL J Mol Biol. 1995 Jun 9;249(3):665-74. PMID:7783219<ref>PMID:7783219</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nhk" 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 25232]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Nucleoside-diphosphate kinase~~]]	+	[[Category: Myxococcus xanthus]]
-	[[Category: Strelkov, S]]	+	[[Category: Strelkov S]]
-	[[Category: Williams~~, R L]]~~	+	[[Category: Williams RL]]
-	~~[[Category: Phosphotransferase~~]]	+

OCA at 08:50, 2 December 2020

2020-12-02T08:50:33Z

←Older revision		Revision as of 08:50, 2 December 2020
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	==CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION==		==CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION==
-	<StructureSection load='1nhk' size='340' side='right' caption='[[1nhk]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1nhk' size='340' side='right'caption='[[1nhk]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nhk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25232 Atcc 25232]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NHK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nhk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25232 Atcc 25232]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NHK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34 ATCC 25232])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34 ATCC 25232])</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=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [http://pdbe.org/1nhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [http://www.ebi.ac.uk/pdbsum/1nhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nhk ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [http://pdbe.org/1nhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [http://www.ebi.ac.uk/pdbsum/1nhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nhk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1nhk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nhk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nucleoside diphosphate kinase 3D structures\|Nucleoside diphosphate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 25232]]		[[Category: Atcc 25232]]
		+	[[Category: Large Structures]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Strelkov, S]]		[[Category: Strelkov, S]]
	[[Category: Williams, R L]]		[[Category: Williams, R L]]
	[[Category: Phosphotransferase]]		[[Category: Phosphotransferase]]

OCA at 07:27, 7 February 2018

2018-02-07T07:27:43Z

←Older revision		Revision as of 07:27, 7 February 2018
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION==		==CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION==
	<StructureSection load='1nhk' size='340' side='right' caption='[[1nhk]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1nhk' size='340' side='right' caption='[[1nhk]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34 ATCC 25232])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34 ATCC 25232])</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=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [http://pdbe.org/1nhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [http://www.ebi.ac.uk/pdbsum/1nhk 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=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [http://pdbe.org/1nhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [http://www.ebi.ac.uk/pdbsum/1nhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nhk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nh/1nhk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nh/1nhk_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1nhk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nhk" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:18, 9 February 2016

2016-02-09T08:18:21Z

←Older revision		Revision as of 08:18, 9 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nhk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:22, 10 September 2015

2015-09-10T20:22:33Z

←Older revision		Revision as of 20:22, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1nhk' size='340' side='right' caption='[[1nhk]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1nhk' size='340' side='right' caption='[[1nhk]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nhk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Myxococcus_xanthus Myxococcus xanthus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NHK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nhk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25232 Atcc 25232]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NHK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34 ~~Myxococcus xanthus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34 ATCC 25232])</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=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [http://www.ebi.ac.uk/pdbsum/1nhk 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=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [http://pdbe.org/1nhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [http://www.ebi.ac.uk/pdbsum/1nhk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1nhk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Myxococcus xanthus~~]]	+	[[Category: Atcc 25232]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Strelkov, S]]		[[Category: Strelkov, S]]
	[[Category: Williams, R L]]		[[Category: Williams, R L]]
	[[Category: Phosphotransferase]]		[[Category: Phosphotransferase]]

OCA at 05:39, 25 December 2014

2014-12-25T05:39:08Z

←Older revision		Revision as of 05:39, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nhk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NHK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nhk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NHK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34 Myxococcus xanthus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34 Myxococcus xanthus])</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=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [http://www.ebi.ac.uk/pdbsum/1nhk 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=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [http://www.ebi.ac.uk/pdbsum/1nhk PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NDK_MYXXA NDK_MYXXA]] Major role in the synthesis of nucleoside triphosphates other than ATP.[HAMAP-Rule:MF_00451]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Myxococcus xanthus]]		[[Category: Myxococcus xanthus]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
-	[[Category: Strelkov, S.]]	+	[[Category: Strelkov, S]]
-	[[Category: Williams, R L.]]	+	[[Category: Williams, R L]]
	[[Category: Phosphotransferase]]		[[Category: Phosphotransferase]]

OCA at 16:11, 28 September 2014

2014-09-28T16:11:02Z

←Older revision		Revision as of 16:11, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1nhk.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION==
		+	<StructureSection load='1nhk' size='340' side='right' caption='[[1nhk]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nhk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NHK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMP:ADENOSINE-3,5-CYCLIC-MONOPHOSPHATE'>CMP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CMP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=34 Myxococcus xanthus])</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=1nhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nhk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nhk RCSB], [http://www.ebi.ac.uk/pdbsum/1nhk 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/nh/1nhk_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The X-ray structure of Myxococcus xanthus nucleoside diphosphate (NDP) kinase complexed with adenosine 3',5'-cyclic monophosphate (cAMP) has been determined. The structure was solved by difference Fourier analysis. The refined structure has a crystallographic R-factor of 0.17 at 1.9 A resolution. The phosphoryl group and ribose moiety make extensive polar interactions with the protein, whereas the base interacts only with two hydrophobic residues. The comparison with the structure of the enzyme complex with the substrate adenosine diphosphate (ADP) reported earlier shows that cAMP and ADP interact similarly with the enzyme. The base of the cAMP is present in two conformations, syn and anti, with respect to the sugar. The syn conformer is dominant. Based on the effect of cAMP on phosphorylation of the human NDP kinase NM23, it had been proposed that cAMP might interact with NDP kinase in a manner distinct from other nucleotides. However, the structure of the M. xanthus NDP kinase/cAMP complex indicates that the nucleotide is a competitive inhibitor of the enzyme and occupies the usual nucleotide site. Kinetic assays of the NDP kinase activity in the presence of cAMP were done. Their results are consistent with a competitive character of the cAMP inhibition.

-	~~{{STRUCTURE_1nhk\| PDB=1nhk \| SCENE= }}~~	+	The 1.9 A crystal structure of a nucleoside diphosphate kinase complex with adenosine 3',5'-cyclic monophosphate: evidence for competitive inhibition.,Strelkov SV, Perisic O, Webb PA, Williams RL J Mol Biol. 1995 Jun 9;249(3):665-74. PMID:7783219<ref>PMID:7783219</ref>

-	~~===CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7783219}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1nhk]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Myxococcus_xanthus Myxococcus xanthus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA].~~	+

	==See Also==		==See Also==
	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]		*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:007783219<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Myxococcus xanthus]]		[[Category: Myxococcus xanthus]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]

OCA at 13:15, 20 October 2012

2012-10-20T13:15:00Z

←Older revision		Revision as of 13:15, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1nhk]] is a 2 chain structure ~~of [[Nucleoside diphosphate kinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA].	+	[[1nhk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA].

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

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

2012-07-26T11:21:50Z

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

←Older revision

Revision as of 11:21, 26 July 2012

OCA at 11:21, 26 July 2012

2012-07-26T11:21:48Z

←Older revision		Revision as of 11:21, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1nhk.png\|left\|200px]]		[[Image:1nhk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1nhk", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1nhk\| PDB=1nhk \| SCENE= }}		{{STRUCTURE_1nhk\| PDB=1nhk \| SCENE= }}

	===CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION===		===CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE SUBSTRATE AT 2.0 ANGSTROMS RESOLUTION===

-		+	{{ABSTRACT_PUBMED_7783219}}
-	~~<!--~~	+
-	~~The line below this paragraph,~~ {{~~ABSTRACT_PUBMED_8263923}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at http://www.pubmed.gov), where 8263923 is the PubMed ID number.~~	+
-	~~-->~~	+
-	~~{{ABSTRACT_PUBMED_8263923~~}}	+

	==About this Structure==		==About this Structure==
-	~~1NHK~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA].	+	[[1nhk]] is a 2 chain structure of [[Nucleoside diphosphate kinase]] with sequence from [http://en.wikipedia.org/wiki/Myxococcus_xanthus Myxococcus xanthus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NHK OCA].
		+
		+	==See Also==
		+	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8263923~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:007783219</ref><references group="xtra"/>
	[[Category: Myxococcus xanthus]]		[[Category: Myxococcus xanthus]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
Line 29:		Line 20:
	[[Category: Williams, R L.]]		[[Category: Williams, R L.]]
	[[Category: Phosphotransferase]]		[[Category: Phosphotransferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:17:51 2009''