3fbe - Revision history

OCA at 06:44, 6 September 2023

2023-09-06T06:44:11Z

←Older revision		Revision as of 06:44, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3fbe' size='340' side='right'caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3fbe' size='340' side='right'caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Apmv Apmv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FBE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FBE 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>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.4Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2b8p\|2b8p]]</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MIMI_R418, NDK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~212035 APMV])</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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [https://pdbe.org/3fbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [https://www.ebi.ac.uk/pdbsum/3fbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbe 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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [https://pdbe.org/3fbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [https://www.ebi.ac.uk/pdbsum/3fbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NDK_MIMIV NDK_MIMIV]] Plays a role in the synthesis of nucleoside triphosphates. This activity may optimize the replication of the AT-rich (73%) viral genome in a thymidine-limited host environment.	+	[https://www.uniprot.org/uniprot/NDK_MIMIV NDK_MIMIV] Plays a role in the synthesis of nucleoside triphosphates. This activity may optimize the replication of the AT-rich (73%) viral genome in a thymidine-limited host environment.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Apmv~~]]	+	[[Category: Acanthamoeba polyphaga mimivirus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Nucleoside-diphosphate kinase]]~~	+	[[Category: Abergel C]]
-	[[Category: Abergel, C]]	+	[[Category: Claverie JM]]
-	[[Category: Claverie~~, J M~~]]	+	[[Category: Jeudy S]]
-	[[Category: Jeudy, S]]	+	[[Category: Lartigue A]]
-	[[Category: Lartigue, A]]	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nucleotide metabolism]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Phosphotransferase nucleotide binding]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 19:52, 20 October 2021

2021-10-20T19:52:35Z

←Older revision		Revision as of 19:52, 20 October 2021
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	<StructureSection load='3fbe' size='340' side='right'caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3fbe' size='340' side='right'caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FBE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FBE 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b8p\|2b8p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b8p\|2b8p]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [~~http~~://pdbe.org/3fbe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fbe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbe 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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [https://pdbe.org/3fbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [https://www.ebi.ac.uk/pdbsum/3fbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NDK_MIMIV NDK_MIMIV]] Plays a role in the synthesis of nucleoside triphosphates. This activity may optimize the replication of the AT-rich (73%) viral genome in a thymidine-limited host environment.	+	[[https://www.uniprot.org/uniprot/NDK_MIMIV NDK_MIMIV]] Plays a role in the synthesis of nucleoside triphosphates. This activity may optimize the replication of the AT-rich (73%) viral genome in a thymidine-limited host environment.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==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 08:06, 24 July 2019

2019-07-24T08:06:47Z

←Older revision		Revision as of 08:06, 24 July 2019
Line 1:		Line 1:

	==Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP==		==Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP==
-	<StructureSection load='3fbe' size='340' side='right' caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3fbe' size='340' side='right'caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBE FirstGlance]. <br>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Apmv]]		[[Category: Apmv]]
		+	[[Category: Large Structures]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Abergel, C]]		[[Category: Abergel, C]]

OCA at 07:15, 5 December 2018

2018-12-05T07:15:18Z

←Older revision		Revision as of 07:15, 5 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP==		==Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP==
	<StructureSection load='3fbe' size='340' side='right' caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3fbe' size='340' side='right' caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [http://pdbe.org/3fbe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [http://www.ebi.ac.uk/pdbsum/3fbe 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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [http://pdbe.org/3fbe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [http://www.ebi.ac.uk/pdbsum/3fbe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbe ProSAT]</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/fb/3fbe_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fb/3fbe_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 19:48, 9 February 2016

2016-02-09T19:48:04Z

←Older revision		Revision as of 19:48, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3fbe' size='340' side='right' caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3fbe' size='340' side='right' caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBE 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b8p\|2b8p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b8p\|2b8p]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 ~~Acanthamoeba polyphaga mimivirus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [http://www.ebi.ac.uk/pdbsum/3fbe 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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [http://pdbe.org/3fbe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [http://www.ebi.ac.uk/pdbsum/3fbe PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3fbe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3fbe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acanthamoeba polyphaga mimivirus~~]]	+	[[Category: Apmv]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Abergel, C]]		[[Category: Abergel, C]]

OCA at 09:08, 25 December 2014

2014-12-25T09:08:25Z

←Older revision		Revision as of 09:08, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBE 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b8p\|2b8p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b8p\|2b8p]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 Acanthamoeba polyphaga mimivirus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 Acanthamoeba polyphaga mimivirus])</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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [http://www.ebi.ac.uk/pdbsum/3fbe 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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [http://www.ebi.ac.uk/pdbsum/3fbe PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NDK_MIMIV NDK_MIMIV]] Plays a role in the synthesis of nucleoside triphosphates. This activity may optimize the replication of the AT-rich (73%) viral genome in a thymidine-limited host environment.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Acanthamoeba polyphaga mimivirus]]		[[Category: Acanthamoeba polyphaga mimivirus]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
-	[[Category: Abergel, C.]]	+	[[Category: Abergel, C]]
-	[[Category: Claverie, J M.]]	+	[[Category: Claverie, J M]]
-	[[Category: Jeudy, S.]]	+	[[Category: Jeudy, S]]
-	[[Category: Lartigue, A.]]	+	[[Category: Lartigue, A]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Kinase]]		[[Category: Kinase]]

OCA at 10:48, 29 September 2014

2014-09-29T10:48:24Z

←Older revision		Revision as of 10:48, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3fbe.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP==
		+	<StructureSection load='3fbe' size='340' side='right' caption='[[3fbe]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBE 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b8p\|2b8p]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 Acanthamoeba polyphaga mimivirus])</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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [http://www.ebi.ac.uk/pdbsum/3fbe 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/fb/3fbe_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 analysis of the Acanthamoeba polyphaga mimivirus genome revealed the first virus-encoded nucleoside diphosphate kinase (NDK), an enzyme that is central to the synthesis of RNA and DNA, ubiquitous in cellular organisms, and well conserved among the three domains of life. In contrast with the broad specificity of cellular NDKs for all types of ribo- and deoxyribonucleotides, the mimivirus enzyme exhibits a strongly preferential affinity for deoxypyrimidines. In order to elucidate the molecular basis of this unique substrate specificity, we determined the three-dimensional (3D) structure of the Acanthamoeba polyphaga mimivirus NDK alone and in complex with various nucleotides. As predicted from a sequence comparison with cellular NDKs, the 3D structure of the mimivirus enzyme exhibits a shorter Kpn loop, previously recognized as a main feature of the NDK active site. The structure of the viral enzyme in complex with various nucleotides also pinpointed two residue changes, both located near the active site and specific to the viral NDK, which could explain its stronger affinity for deoxynucleotides and pyrimidine nucleotides. The role of these residues was explored by building a set of viral NDK variants, assaying their enzymatic activities, and determining their 3D structures in complex with various nucleotides. A total of 26 crystallographic structures were determined at resolutions ranging from 2.8 A to 1.5 A. Our results suggest that the mimivirus enzyme progressively evolved from an ancestral NDK under the constraints of optimizing its efficiency for the replication of an AT-rich (73%) viral genome in a thymidine-limited host environment.

-	~~{{STRUCTURE_3fbe\| PDB=3fbe \| SCENE= }}~~	+	Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.,Jeudy S, Lartigue A, Claverie JM, Abergel C J Virol. 2009 Jul;83(14):7142-50. Epub 2009 May 13. PMID:19439473<ref>PMID:19439473</ref>

-	~~===Crystal structure~~ of the ~~Mimivirus NDK N62L-R107G double mutant complexed with GDP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19439473}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3fbe]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA].~~	+

	==See Also==		==See Also==
	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]		*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019439473<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Acanthamoeba polyphaga mimivirus]]		[[Category: Acanthamoeba polyphaga mimivirus]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]

OCA at 14:56, 20 October 2012

2012-10-20T14:56:17Z

←Older revision		Revision as of 14:56, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3fbe]] is a 6 chain structure ~~of [[Nucleoside diphosphate kinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA].	+	[[3fbe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA].

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

OCA: Protected "3fbe" [edit=sysop:move=sysop]

2012-07-26T16:45:26Z

Protected "3fbe" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:45, 26 July 2012

OCA at 16:45, 26 July 2012

2012-07-26T16:45:24Z

←Older revision		Revision as of 16:45, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3fbe.png\|left\|200px]]		[[Image:3fbe.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3fbe", 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),
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	{{STRUCTURE_3fbe\| PDB=3fbe \| SCENE= }}		{{STRUCTURE_3fbe\| PDB=3fbe \| SCENE= }}

	===Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP===		===Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19439473}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19439473 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19439473}}		{{ABSTRACT_PUBMED_19439473}}

	==About this Structure==		==About this Structure==
-	~~3FBE~~ is a 6 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA].	+	[[3fbe]] is a 6 chain structure of [[Nucleoside diphosphate kinase]] with sequence from [http://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA].
		+
		+	==See Also==
		+	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19439473~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019439473</ref><references group="xtra"/>
	[[Category: Acanthamoeba polyphaga mimivirus]]		[[Category: Acanthamoeba polyphaga mimivirus]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
Line 39:		Line 30:
	[[Category: Phosphotransferase nucleotide binding]]		[[Category: Phosphotransferase nucleotide binding]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 25 08:21:00 2009''