1x55 - Revision history

OCA at 08:05, 25 October 2023

2023-10-25T08:05:54Z

←Older revision		Revision as of 08:05, 25 October 2023
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	<StructureSection load='1x55' size='340' side='right'caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1x55' size='340' side='right'caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~'pyrococcus_shinkaii' 'pyrococcus shinkaii'~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X55 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=NSS:5-O-~~[~~N-(L-ASPARAGINYL)SULFAMOYL~~]~~ADENOSINE'>NSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1x54\|1x54]], [[1x56\|1x56]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NSS:5-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE'>NSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22]~~ </~~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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [https://pdbe.org/1x55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [https://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x55 ProSAT], [https://www.topsan.org/Proteins/RSGI/1x55 TOPSAN]</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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [https://pdbe.org/1x55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [https://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x55 ProSAT], [https://www.topsan.org/Proteins/RSGI/1x55 TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SYN_PYRHO SYN_PYRHO]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pyrococcus shinkaii]]
-	[[Category: Asparagine--tRNA ligase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Iwasaki, W~~]]	+	[[Category: Pyrococcus horikoshii]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Iwasaki W]]
-	[[Category: Sekine, S]]	+	[[Category: Sekine S]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Aminoacyl-trna synthetase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 16:34, 27 October 2021

2021-10-27T16:34:09Z

←Older revision		Revision as of 16:34, 27 October 2021
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	<StructureSection load='1x55' size='340' side='right'caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1x55' size='340' side='right'caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1X55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X55 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NSS:5-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE'>NSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NSS:5-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE'>NSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x54\|1x54]], [[1x56\|1x56]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1x54\|1x54]], [[1x56\|1x56]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22] </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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [~~http~~://pdbe.org/1x55 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1x55 ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1x55 TOPSAN]</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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [https://pdbe.org/1x55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [https://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x55 ProSAT], [https://www.topsan.org/Proteins/RSGI/1x55 TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 17:16, 22 January 2020

2020-01-22T17:16:44Z

←Older revision		Revision as of 17:16, 22 January 2020
Line 1:		Line 1:

	==Crystal structure of asparaginyl-tRNA synthetase from Pyrococcus horikoshii complexed with asparaginyl-adenylate analogue==		==Crystal structure of asparaginyl-tRNA synthetase from Pyrococcus horikoshii complexed with asparaginyl-adenylate analogue==
-	<StructureSection load='1x55' size='340' side='right' caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1x55' size='340' side='right'caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X55 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X55 FirstGlance]. <br>
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Aminoacyl tRNA ~~Synthetase~~\|Aminoacyl tRNA ~~Synthetase~~]]	+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	[[Category: Pyrococcus shinkaii]]		[[Category: Pyrococcus shinkaii]]
	[[Category: Asparagine--tRNA ligase]]		[[Category: Asparagine--tRNA ligase]]
		+	[[Category: Large Structures]]
	[[Category: Iwasaki, W]]		[[Category: Iwasaki, W]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 16:03, 11 April 2018

2018-04-11T16:03:15Z

←Older revision		Revision as of 16:03, 11 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of asparaginyl-tRNA synthetase from Pyrococcus horikoshii complexed with asparaginyl-adenylate analogue==		==Crystal structure of asparaginyl-tRNA synthetase from Pyrococcus horikoshii complexed with asparaginyl-adenylate analogue==
	<StructureSection load='1x55' size='340' side='right' caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1x55' size='340' side='right' caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x54\|1x54]], [[1x56\|1x56]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x54\|1x54]], [[1x56\|1x56]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22] </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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [http://pdbe.org/1x55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [http://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [http://www.topsan.org/Proteins/RSGI/1x55 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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [http://pdbe.org/1x55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [http://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1x55 ProSAT], [http://www.topsan.org/Proteins/RSGI/1x55 TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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/x5/1x55_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x5/1x55_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 02:37, 10 February 2016

2016-02-10T02:37:15Z

←Older revision		Revision as of 02:37, 10 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1x55 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:33, 11 September 2015

2015-09-11T04:33:03Z

←Older revision		Revision as of 04:33, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1x55' size='340' side='right' caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1x55' size='340' side='right' caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii Pyrococcus horikoshii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X55 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NSS:5-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE'>NSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NSS:5-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE'>NSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x54\|1x54]], [[1x56\|1x56]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x54\|1x54]], [[1x56\|1x56]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22] </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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [http://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [http://www.topsan.org/Proteins/RSGI/1x55 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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [http://pdbe.org/1x55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [http://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [http://www.topsan.org/Proteins/RSGI/1x55 TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1x55" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pyrococcus shinkaii]]
	[[Category: Asparagine--tRNA ligase]]		[[Category: Asparagine--tRNA ligase]]
-	[[Category: Pyrococcus horikoshii]]
	[[Category: Iwasaki, W]]		[[Category: Iwasaki, W]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 12:22, 6 January 2015

2015-01-06T12:22:50Z

←Older revision		Revision as of 12:22, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X55 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X55 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NSS:5-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE'>NSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NSS:5-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE'>NSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x54\|1x54]], [[1x56\|1x56]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x54\|1x54]], [[1x56\|1x56]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22] </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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [http://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [http://www.topsan.org/Proteins/RSGI/1x55 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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [http://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [http://www.topsan.org/Proteins/RSGI/1x55 TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: Asparagine--tRNA ligase]]		[[Category: Asparagine--tRNA ligase]]
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
-	[[Category: Iwasaki, W.]]	+	[[Category: Iwasaki, W]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sekine, S.]]	+	[[Category: Sekine, S]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Aminoacyl-trna synthetase]]		[[Category: Aminoacyl-trna synthetase]]
	[[Category: Ligase]]		[[Category: Ligase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 19:20, 28 September 2014

2014-09-28T19:20:19Z

←Older revision		Revision as of 19:20, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1x55.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of asparaginyl-tRNA synthetase from Pyrococcus horikoshii complexed with asparaginyl-adenylate analogue==
		+	<StructureSection load='1x55' size='340' side='right' caption='[[1x55]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X55 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NSS:5-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE'>NSS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x54\|1x54]], [[1x56\|1x56]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparagine--tRNA_ligase Asparagine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.22 6.1.1.22] </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=1x55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x55 RCSB], [http://www.ebi.ac.uk/pdbsum/1x55 PDBsum], [http://www.topsan.org/Proteins/RSGI/1x55 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/x5/1x55_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 ==
		+	Asparaginyl-tRNA synthetase (AsnRS) is a member of the class-II aminoacyl-tRNA synthetases, and is responsible for catalyzing the specific aminoacylation of tRNA(Asn) with asparagine. Here, the crystal structure of AsnRS from Pyrococcus horikoshii, complexed with asparaginyl-adenylate (Asn-AMP), was determined at 1.45 A resolution, and those of free AsnRS and AsnRS complexed with an Asn-AMP analog (Asn-SA) were solved at 1.98 and 1.80 A resolutions, respectively. All of the crystal structures have many solvent molecules, which form a network of hydrogen-bonding interactions that surrounds the entire AsnRS molecule. In the AsnRS/Asn-AMP complex (or the AsnRS/Asn-SA), one side of the bound Asn-AMP (or Asn-SA) is completely covered by the solvent molecules, which complement the binding site. In particular, two of these water molecules were found to interact directly with the asparagine amide and carbonyl groups, respectively, and to contribute to the formation of a pocket highly complementary to the asparagine side-chain. Thus, these two water molecules appear to play a key role in the strict recognition of asparagine and the discrimination against aspartic acid by the AsnRS. This water-assisted asparagine recognition by the AsnRS strikingly contrasts with the fact that the aspartic acid recognition by the closely related aspartyl-tRNA synthetase is achieved exclusively through extensive interactions with protein amino acid residues. Furthermore, based on a docking model of AsnRS and tRNA, a single arginine residue (Arg83) in the AsnRS was postulated to be involved in the recognition of the third position of the tRNA(Asn) anticodon (U36). We performed a mutational analysis of this particular arginine residue, and confirmed its significance in the tRNA recognition.

-	~~{{STRUCTURE_1x55\| PDB=1x55 \| SCENE= }}~~	+	Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase.,Iwasaki W, Sekine S, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S J Mol Biol. 2006 Jul 7;360(2):329-42. Epub 2006 May 15. PMID:16753178<ref>PMID:16753178</ref>

-	~~===Crystal structure~~ of ~~asparaginyl-tRNA synthetase from Pyrococcus horikoshii complexed with asparaginyl-adenylate analogue===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16753178}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1x55]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA].~~	+

	==See Also==		==See Also==
	*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]		*[[Aminoacyl tRNA Synthetase\|Aminoacyl tRNA Synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016753178<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Asparagine--tRNA ligase]]		[[Category: Asparagine--tRNA ligase]]
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]

OCA at 16:01, 20 October 2012

2012-10-20T16:01:59Z

←Older revision		Revision as of 16:01, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1x55]] is a 1 chain structure ~~of [[Aminoacyl tRNA Synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA].	+	[[1x55]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X55 OCA].

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

OCA: Protected "1x55" [edit=sysop:move=sysop]

2012-07-26T20:21:59Z

Protected "1x55" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:21, 26 July 2012