1iow - Revision history

OCA at 06:27, 9 August 2023

2023-08-09T06:27:03Z

←Older revision		Revision as of 06:27, 9 August 2023
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	<StructureSection load='1iow' size='340' side='right'caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1iow' size='340' side='right'caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IOW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IOW 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </span></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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene></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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [https://pdbe.org/1iow PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [https://www.ebi.ac.uk/pdbsum/1iow PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iow 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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [https://pdbe.org/1iow PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [https://www.ebi.ac.uk/pdbsum/1iow PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iow ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DDLB_ECOLI DDLB_ECOLI]] Cell wall formation.	+	[https://www.uniprot.org/uniprot/DDLB_ECOLI DDLB_ECOLI] Cell wall formation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: D-alanine--D-alanine ligase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fan, C]]	+	[[Category: Fan C]]
-	[[Category: Knox~~, J R~~]]	+	[[Category: Knox JR]]
-	[[Category: Moews~~, P C]]~~	+	[[Category: Moews PC]]
-	~~[[Category: Adp binding]]~~	+
-	~~[[Category: Cell wall]]~~	+
-	~~[[Category: Glycogen phosphorylase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Peptidoglycan synthesis]]~~	+
-	~~[[Category: Vancomycin~~]]	+

OCA at 11:03, 4 August 2021

2021-08-04T11:03:01Z

←Older revision		Revision as of 11:03, 4 August 2021
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	<StructureSection load='1iow' size='340' side='right'caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1iow' size='340' side='right'caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1IOW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IOW 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [~~http~~://pdbe.org/1iow PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1iow PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1iow 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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [https://pdbe.org/1iow PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [https://www.ebi.ac.uk/pdbsum/1iow PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iow ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DDLB_ECOLI DDLB_ECOLI]] Cell wall formation.	+	[[https://www.uniprot.org/uniprot/DDLB_ECOLI DDLB_ECOLI]] Cell wall formation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:57, 30 October 2019

2019-10-30T09:57:04Z

←Older revision		Revision as of 09:57, 30 October 2019
Line 1:		Line 1:

	==COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE==		==COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE==
-	<StructureSection load='1iow' size='340' side='right' caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1iow' size='340' side='right'caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IOW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IOW FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1iow" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1iow" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[D-alanine-D-alanine ligase 3D structures\|D-alanine-D-alanine ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: D-alanine--D-alanine ligase]]		[[Category: D-alanine--D-alanine ligase]]
		+	[[Category: Large Structures]]
	[[Category: Fan, C]]		[[Category: Fan, C]]
	[[Category: Knox, J R]]		[[Category: Knox, J R]]

OCA at 08:43, 17 January 2018

2018-01-17T08:43:27Z

←Older revision		Revision as of 08:43, 17 January 2018
Line 1:		Line 1:
		+
	==COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE==		==COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE==
	<StructureSection load='1iow' size='340' side='right' caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1iow' size='340' side='right' caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 5:		Line 6:
	</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [http://pdbe.org/1iow PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [http://www.ebi.ac.uk/pdbsum/1iow 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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [http://pdbe.org/1iow PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [http://www.ebi.ac.uk/pdbsum/1iow PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1iow ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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/io/1iow_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/io/1iow_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1iow" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1iow" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[D-alanine-D-alanine ligase\|D-alanine-D-alanine ligase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:18, 7 February 2016

2016-02-07T16:18:24Z

←Older revision		Revision as of 16:18, 7 February 2016
Line 17:		Line 17:
	<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=1iow ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:09, 10 September 2015

2015-09-10T03:09:51Z

←Older revision		Revision as of 03:09, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1iow' size='340' side='right' caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1iow' size='340' side='right' caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IOW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IOW 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [http://www.ebi.ac.uk/pdbsum/1iow 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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [http://pdbe.org/1iow PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [http://www.ebi.ac.uk/pdbsum/1iow PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1iow" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: D-alanine--D-alanine ligase]]		[[Category: D-alanine--D-alanine ligase]]
-	[[Category: Escherichia coli]]
	[[Category: Fan, C]]		[[Category: Fan, C]]
	[[Category: Knox, J R]]		[[Category: Knox, J R]]

OCA at 16:37, 24 December 2014

2014-12-24T16:37:34Z

←Older revision		Revision as of 16:37, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IOW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IOW 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [http://www.ebi.ac.uk/pdbsum/1iow 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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [http://www.ebi.ac.uk/pdbsum/1iow PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDLB_ECOLI DDLB_ECOLI]] Cell wall formation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: D-alanine--D-alanine ligase]]		[[Category: D-alanine--D-alanine ligase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Fan, C.]]	+	[[Category: Fan, C]]
-	[[Category: Knox, J R.]]	+	[[Category: Knox, J R]]
-	[[Category: Moews, P C.]]	+	[[Category: Moews, P C]]
	[[Category: Adp binding]]		[[Category: Adp binding]]
	[[Category: Cell wall]]		[[Category: Cell wall]]

OCA at 13:57, 28 September 2014

2014-09-28T13:57:58Z

←Older revision		Revision as of 13:57, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1iow.~~png\|left~~\|200px]]	+	==COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE==
		+	<StructureSection load='1iow' size='340' side='right' caption='[[1iow]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1iow]] 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=1IOW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IOW 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHY:1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC+ACID'>PHY</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </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=1iow FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iow OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iow RCSB], [http://www.ebi.ac.uk/pdbsum/1iow 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/io/1iow_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 crystallographic structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli complexed with a D-Ala-D-alpha-hydroxybutyrate phosphonate and the structure of the Y216F mutant ligase complexed with a D-Ala-D-Ala phosphinate have been determined to 2.2 and 1.9 A resolution, respectively, and refined to R factors of 0.156 and 0.158. In each complex the inhibitor has reacted with ATP to produce ADP and a tight-binding phosphorylated transition state intermediate. Comparison of these two structures with the known crystal structure of the phosphinate intermediate of the wild-type ligase shows no major conformational changes, but B factors indicate differences in mobility of loops covering the binding site. The weaker inhibition of the Y216F mutant by both inhibitors is thought to be due in part to the loss of an interloop hydrogen bond. A similar mechanism may account for poor inhibition of VanA, the homologous D-Ala:D-lactate ligase produced by vancomycin-resistant enterococci.

-	~~{{STRUCTURE_1iow\| PDB=1iow \| SCENE= }}~~	+	D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant.,Fan C, Park IS, Walsh CT, Knox JR Biochemistry. 1997 Mar 4;36(9):2531-8. PMID:9054558<ref>PMID:9054558</ref>

-	~~===COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_9054558}}~~	+	==See Also==
-		+	*[[D-alanine-D-alanine ligase\|D-alanine-D-alanine ligase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1iow~~]] 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=1IOW OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:009054558<~~/~~ref~~><~~ref group="xtra">PMID:009605318</ref><ref group="xtra">PMID:011742118</ref><references group="xtra"~~/>	+
	[[Category: D-alanine--D-alanine ligase]]		[[Category: D-alanine--D-alanine ligase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

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

2012-11-28T14:57:14Z

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

←Older revision

Revision as of 14:57, 28 November 2012

OCA at 14:57, 28 November 2012

2012-11-28T14:57:13Z

←Older revision		Revision as of 14:57, 28 November 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1iow.png\|left\|200px]]		[[Image:1iow.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1iow", 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_1iow\| PDB=1iow \| SCENE= }}		{{STRUCTURE_1iow\| PDB=1iow \| SCENE= }}

	===COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE===		===COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9054558}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9054558 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9054558}}		{{ABSTRACT_PUBMED_9054558}}

	==About this Structure==		==About this Structure==
-	~~1IOW~~ 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=1IOW OCA].	+	[[1iow]] 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=1IOW OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9054558~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009054558</ref><ref group="xtra">PMID:009605318</ref><ref group="xtra">PMID:011742118</ref><references group="xtra"/>
	[[Category: D-alanine--D-alanine ligase]]		[[Category: D-alanine--D-alanine ligase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 35:		Line 23:
	[[Category: Peptidoglycan synthesis]]		[[Category: Peptidoglycan synthesis]]
	[[Category: Vancomycin]]		[[Category: Vancomycin]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:03:17 2009''