2jfg - Revision history

OCA at 14:46, 13 December 2023

2023-12-13T14:46:15Z

←Older revision		Revision as of 14:46, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2jfg' size='340' side='right'caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='2jfg' size='340' side='right'caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JFG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JFG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</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]] 1.52Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~KCX~~:~~LYSINE+NZ~~-~~CARBOXYLIC+ACID~~'>~~KCX~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/UDP~~-N-~~acetylmuramoyl-L-alanine--D-glutamate_ligase UDP~~-N-~~acetylmuramoyl~~-L-~~alanine--D-glutamate ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9]~~ </~~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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [https://pdbe.org/2jfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [https://www.ebi.ac.uk/pdbsum/2jfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jfg 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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [https://pdbe.org/2jfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [https://www.ebi.ac.uk/pdbsum/2jfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jfg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MURD_ECOLI MURD_ECOLI] Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA).[HAMAP-Rule:MF_00639]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]~~	+	[[Category: Blanot D]]
-	[[Category: Blanot, D]]	+	[[Category: Contreras-Martel C]]
-	[[Category: Contreras-Martel, C]]	+	[[Category: Dessen A]]
-	[[Category: Dessen, A]]	+	[[Category: Gobec S]]
-	[[Category: Gobec, S]]	+	[[Category: Herve M]]
-	[[Category: Herve, M]]	+	[[Category: Humljan J]]
-	[[Category: Humljan, J]]	+	[[Category: Kotnik M]]
-	[[Category: Kotnik, M]]	+	[[Category: Kristan K]]
-	[[Category: Kristan, K]]	+	[[Category: Oblak M]]
-	[[Category: Oblak, M]]	+	[[Category: Solmajer T]]
-	[[Category: Solmajer, T]]	+	[[Category: Urleb U]]
-	[[Category: Urleb, U]]	+
-	~~[[Category: Adp]]~~	+
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Cell cycle]]~~	+
-	~~[[Category: Cell division]]~~	+
-	~~[[Category: Cell shape]]~~	+
-	~~[[Category: Cell wall]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Murd ligase]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Peptidoglycan synthesis]]~~	+
-	~~[[Category: Uma~~]]	+

OCA at 20:45, 20 October 2021

2021-10-20T20:45:13Z

←Older revision		Revision as of 20:45, 20 October 2021
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	<StructureSection load='2jfg' size='340' side='right'caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='2jfg' size='340' side='right'caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2JFG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JFG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [~~http~~://pdbe.org/2jfg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2jfg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2jfg 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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [https://pdbe.org/2jfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [https://www.ebi.ac.uk/pdbsum/2jfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jfg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 19:10, 11 December 2019

2019-12-11T19:10:42Z

←Older revision		Revision as of 19:10, 11 December 2019
Line 1:		Line 1:

	==Crystal structure of MurD ligase in complex with UMA and ADP==		==Crystal structure of MurD ligase in complex with UMA and ADP==
-	<StructureSection load='2jfg' size='340' side='right' caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>	+	<StructureSection load='2jfg' size='340' side='right'caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JFG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JFG FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2jfg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2jfg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Mur ligase\|Mur ligase]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
	[[Category: Blanot, D]]		[[Category: Blanot, D]]

OCA at 06:39, 31 January 2018

2018-01-31T06:39:16Z

←Older revision		Revision as of 06:39, 31 January 2018
Line 1:		Line 1:
-	==~~CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH~~ UMA ~~AND~~ ADP==	+
		+	==Crystal structure of MurD ligase in complex with UMA and ADP==
	<StructureSection load='2jfg' size='340' side='right' caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='2jfg' size='340' side='right' caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [http://pdbe.org/2jfg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [http://www.ebi.ac.uk/pdbsum/2jfg 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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [http://pdbe.org/2jfg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [http://www.ebi.ac.uk/pdbsum/2jfg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jfg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jf/2jfg_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jf/2jfg_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>
	</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=2jfg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2jfg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2jfg" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[MurD ligase\|MurD ligase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:28, 12 September 2015

2015-09-12T00:28:05Z

←Older revision		Revision as of 00:28, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2jfg' size='340' side='right' caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='2jfg' size='340' side='right' caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JFG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JFG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [http://www.ebi.ac.uk/pdbsum/2jfg 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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [http://pdbe.org/2jfg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [http://www.ebi.ac.uk/pdbsum/2jfg PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 2jfg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
	[[Category: Blanot, D]]		[[Category: Blanot, D]]

OCA at 15:00, 19 January 2015

2015-01-19T15:00:55Z

←Older revision		Revision as of 15:00, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JFG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JFG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [http://www.ebi.ac.uk/pdbsum/2jfg 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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [http://www.ebi.ac.uk/pdbsum/2jfg PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
-	[[Category: Blanot, D.]]	+	[[Category: Blanot, D]]
-	[[Category: Contreras-Martel, C.]]	+	[[Category: Contreras-Martel, C]]
-	[[Category: Dessen, A.]]	+	[[Category: Dessen, A]]
-	[[Category: Gobec, S.]]	+	[[Category: Gobec, S]]
-	[[Category: Herve, M.]]	+	[[Category: Herve, M]]
-	[[Category: Humljan, J.]]	+	[[Category: Humljan, J]]
-	[[Category: Kotnik, M.]]	+	[[Category: Kotnik, M]]
-	[[Category: Kristan, K.]]	+	[[Category: Kristan, K]]
-	[[Category: Oblak, M.]]	+	[[Category: Oblak, M]]
-	[[Category: Solmajer, T.]]	+	[[Category: Solmajer, T]]
-	[[Category: Urleb, U.]]	+	[[Category: Urleb, U]]
	[[Category: Adp]]		[[Category: Adp]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA at 08:31, 30 September 2014

2014-09-30T08:31:25Z

←Older revision		Revision as of 08:31, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2jfg.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP==
		+	<StructureSection load='2jfg' size='340' side='right' caption='[[2jfg]], [[Resolution\|resolution]] 1.52Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2jfg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JFG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e0d\|1e0d]], [[1eeh\|1eeh]], [[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]], [[2jff\|2jff]], [[2jfh\|2jfh]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=2jfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jfg RCSB], [http://www.ebi.ac.uk/pdbsum/2jfg 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/jf/2jfg_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 ==
		+	Mur ligases play an essential role in the intracellular biosynthesis of bacterial peptidoglycan, the main component of the bacterial cell wall, and represent attractive targets for the design of novel antibacterials. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) catalyses the addition of D-glutamic acid to the cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine (UMA) and is the second in the series of Mur ligases. MurD ligase is highly stereospecific for its substrate, D-glutamic acid (D-Glu). Here, we report the high resolution crystal structures of MurD in complexes with two novel inhibitors designed to mimic the transition state of the reaction, which contain either the D-Glu or the L-Glu moiety. The binding modes of N-sulfonyl-D-Glu and N-sulfonyl-L-Glu derivatives were also characterised kinetically. The results of this study represent an excellent starting point for further development of novel inhibitors of this enzyme.

-	~~{{STRUCTURE_2jfg\| PDB=2jfg \| SCENE= }}~~	+	Structural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase.,Kotnik M, Humljan J, Contreras-Martel C, Oblak M, Kristan K, Herve M, Blanot D, Urleb U, Gobec S, Dessen A, Solmajer T J Mol Biol. 2007 Jun 29;370(1):107-15. Epub 2007 May 4. PMID:17507028<ref>PMID:17507028</ref>

-	~~===CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_17507028}}~~	+	==See Also==
-		+	*[[MurD ligase\|MurD ligase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2jfg~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:017507028<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]

OCA: Protected "2jfg" [edit=sysop:move=sysop]

2013-01-07T13:31:35Z

Protected "2jfg" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:31, 7 January 2013

OCA at 13:31, 7 January 2013

2013-01-07T13:31:33Z

←Older revision		Revision as of 13:31, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2jfg.png\|left\|200px]]		[[Image:2jfg.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2jfg", 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_2jfg\| PDB=2jfg \| SCENE= }}		{{STRUCTURE_2jfg\| PDB=2jfg \| SCENE= }}

	===CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP===		===CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17507028}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17507028 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17507028}}		{{ABSTRACT_PUBMED_17507028}}

	==About this Structure==		==About this Structure==
-	~~2JFG~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA].	+	[[2jfg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17507028~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017507028</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
Line 48:		Line 36:
	[[Category: Peptidoglycan synthesis]]		[[Category: Peptidoglycan synthesis]]
	[[Category: Uma]]		[[Category: Uma]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:04:05 2009''

OCA at 06:04, 18 February 2009

2009-02-18T06:04:06Z

←Older revision		Revision as of 06:04, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2JFG is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA].	+	2JFG is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFG OCA].

	==Reference==		==Reference==
-	Structural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase., Kotnik M, Humljan J, Contreras-Martel C, Oblak M, Kristan K, Herve M, Blanot D, Urleb U, Gobec S, Dessen A, Solmajer T, J Mol Biol. 2007 Jun 29;370(1):107-15. Epub 2007 May 4. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17507028 17507028]~~	+	<ref group="xtra">PMID:17507028</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
	[[Category: Blanot, D.]]		[[Category: Blanot, D.]]
Line 50:		Line 49:
	[[Category: Uma]]		[[Category: Uma]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 14~~:31:~~41 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:04:05 2009''