1wkk - Revision history

OCA at 07:56, 25 October 2023

OCA — Wed, 25 Oct 2023 07:56:30 GMT

←Older revision		Revision as of 07:56, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='1wkk' size='340' side='right'caption='[[1wkk]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1wkk' size='340' side='right'caption='[[1wkk]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wkk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1WKK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wkk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GDP:GUANOSINE~~-~~5-DIPHOSPHATE'>GDP</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='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1wkj\|1wkj]], [[1wkl\|1wkl]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~274~~ "~~Flavobacterium thermophilum~~" ~~Yoshida and Oshima 1971])</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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [https://pdbe.org/1wkk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [https://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkk ProSAT], [https://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</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~~://proteopedia.org/fgij/fg.htm?mol=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [~~http~~://pdbe.org/1wkk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkk ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NDK_THET8 NDK_THET8]] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.	+	[https://www.uniprot.org/uniprot/NDK_THET8 NDK_THET8] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Nucleoside-diphosphate kinase~~]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Kuramitsu, S]]	+	[[Category: Kuramitsu S]]
-	[[Category: Masui, R]]	+	[[Category: Masui R]]
-	[[Category: Nakagawa, N]]	+	[[Category: Nakagawa N]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Takeishi S]]
-	[[Category: Takeishi, S]]	+
-	~~[[Category: Complex with gdp]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Nucleoside diphosphate kinase]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Thermus themophilus hb8]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:49, 30 December 2020

OCA — Wed, 30 Dec 2020 07:49:02 GMT

←Older revision		Revision as of 07:49, 30 December 2020
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	==Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP==		==Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP==
-	<StructureSection load='1wkk' size='340' side='right' caption='[[1wkk]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='1wkk' size='340' side='right'caption='[[1wkk]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wkk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WKK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wkk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1WKK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkj\|1wkj]], [[1wkl\|1wkl]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wkj\|1wkj]], [[1wkl\|1wkl]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [http://pdbe.org/1wkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [http://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkk ProSAT], [http://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [http://pdbe.org/1wkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [http://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkk ProSAT], [http://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:

	==See Also==		==See Also==
-	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]	+	*[[Nucleoside diphosphate kinase 3D structures\|Nucleoside diphosphate kinase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Large Structures]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]

OCA at 16:05, 11 April 2018

OCA — Wed, 11 Apr 2018 16:05:08 GMT

←Older revision		Revision as of 16:05, 11 April 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP==		==Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP==
	<StructureSection load='1wkk' size='340' side='right' caption='[[1wkk]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1wkk' size='340' side='right' caption='[[1wkk]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [http://pdbe.org/1wkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [http://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [http://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [http://pdbe.org/1wkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [http://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkk ProSAT], [http://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wk/1wkk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wk/1wkk_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>

OCA at 02:23, 9 February 2016

OCA — Tue, 09 Feb 2016 02:23:42 GMT

←Older revision		Revision as of 02:23, 9 February 2016
Line 19:		Line 19:
	<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=1wkk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>

OCA at 17:41, 10 September 2015

OCA — Thu, 10 Sep 2015 17:41:23 GMT

←Older revision		Revision as of 17:41, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1wkk' size='340' side='right' caption='[[1wkk]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1wkk' size='340' side='right' caption='[[1wkk]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wkk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wkk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkj\|1wkj]], [[1wkl\|1wkl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkj\|1wkj]], [[1wkl\|1wkl]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 ~~Thermus thermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [http://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [http://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [http://pdbe.org/1wkk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [http://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [http://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
-	[[Category: Thermus thermophilus]]
	[[Category: Kuramitsu, S]]		[[Category: Kuramitsu, S]]
	[[Category: Masui, R]]		[[Category: Masui, R]]

OCA at 03:45, 25 December 2014

OCA — Thu, 25 Dec 2014 03:45:40 GMT

←Older revision		Revision as of 03:45, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wkk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKK FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wkk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkj\|1wkj]], [[1wkl\|1wkl]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkj\|1wkj]], [[1wkl\|1wkl]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [http://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [http://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [http://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [http://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NDK_THET8 NDK_THET8]] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		Line 28:
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Kuramitsu, S.]]	+	[[Category: Kuramitsu, S]]
-	[[Category: Masui, R.]]	+	[[Category: Masui, R]]
-	[[Category: Nakagawa, N.]]	+	[[Category: Nakagawa, N]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Takeishi, S.]]	+	[[Category: Takeishi, S]]
	[[Category: Complex with gdp]]		[[Category: Complex with gdp]]
	[[Category: Kinase]]		[[Category: Kinase]]
	[[Category: Nucleoside diphosphate kinase]]		[[Category: Nucleoside diphosphate kinase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Thermus themophilus hb8]]		[[Category: Thermus themophilus hb8]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 20:52, 28 September 2014

OCA — Sun, 28 Sep 2014 20:52:00 GMT

←Older revision		Revision as of 20:52, 28 September 2014
Line 1:		Line 1:
-	~~[[Image:1wkk.png\|left\|200px]]~~	+	==Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP==
-		+	<StructureSection load='1wkk' size='340' side='right' caption='[[1wkk]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~{{STRUCTURE_1wkk\| PDB=1wkk \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[1wkk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WKK FirstGlance]. <br>
-	===Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP===	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wkj\|1wkj]], [[1wkl\|1wkl]]</td></tr>
-		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
-	==~~About this Structure~~==	+	<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>
-	[[1wkk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA].	+	<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=1wkk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wkk RCSB], [http://www.ebi.ac.uk/pdbsum/1wkk PDBsum], [http://www.topsan.org/Proteins/RSGI/1wkk TOPSAN]</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/wk/1wkk_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>

	==See Also==		==See Also==
	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]		*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
		+	__TOC__
		+	</StructureSection>
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 12:18, 20 October 2012

OCA — Sat, 20 Oct 2012 12:18:59 GMT

←Older revision		Revision as of 12:18, 20 October 2012
Line 7:		Line 7:

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

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

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

OCA — Thu, 26 Jul 2012 08:20:00 GMT

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

←Older revision

Revision as of 08:20, 26 July 2012

OCA at 08:19, 26 July 2012

OCA — Thu, 26 Jul 2012 08:19:58 GMT

←Older revision		Revision as of 08:19, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wkk.png\|left\|200px]]		[[Image:1wkk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wkk", 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_1wkk\| PDB=1wkk \| SCENE= }}		{{STRUCTURE_1wkk\| PDB=1wkk \| SCENE= }}

Line 14:		Line 7:

	==About this Structure==		==About this Structure==
-	~~1WKK~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA].	+	[[1wkk]] is a 2 chain structure of [[Nucleoside diphosphate kinase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKK OCA].
		+
		+	==See Also==
		+	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
Line 29:		Line 25:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Thermus themophilus hb8]]		[[Category: Thermus themophilus hb8]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Sun Nov 16 12:03:30 2008''~~	+