1kds - Revision history

OCA at 08:56, 16 August 2023

OCA — Wed, 16 Aug 2023 08:56:25 GMT

←Older revision		Revision as of 08:56, 16 August 2023
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	<StructureSection load='1kds' size='340' side='right'caption='[[1kds]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1kds' size='340' side='right'caption='[[1kds]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kds]] is a 2 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=1KDS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1KDS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kds]] is a 2 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=1KDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NPB:3~~-~~NITROPHENYLBORONIC+ACID'>NPB</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.15Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1c3b\|1c3b]], [[1ga9\|1ga9]], [[3bls\|3bls]], [[1kdw\|1kdw]], [[1ke0\|1ke0]], [[1ke3\|1ke3]], [[1ke4\|1ke4]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NPB:3-NITROPHENYLBORONIC+ACID'>NPB</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [https://pdbe.org/1kds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [https://www.ebi.ac.uk/pdbsum/1kds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kds ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [~~http~~://pdbe.org/1kds PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kds PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kds ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI]] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.	+	[https://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.
	== 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: Beta-lactamase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Powers~~, R A~~]]	+	[[Category: Powers RA]]
-	[[Category: Shoichet~~, B K]]~~	+	[[Category: Shoichet BK]]
-	~~[[Category: Cephalosporinase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phenylboronic acid inhibitor complex]]~~	+
-	~~[[Category: Serine hydrolase~~]]	+

OCA at 07:43, 25 November 2020

OCA — Wed, 25 Nov 2020 07:43:40 GMT

←Older revision		Revision as of 07:43, 25 November 2020
Line 1:		Line 1:

	==X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 3-nitrophenylboronic acid==		==X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 3-nitrophenylboronic acid==
-	<StructureSection load='1kds' size='340' side='right' caption='[[1kds]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='1kds' size='340' side='right'caption='[[1kds]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kds]] is a 2 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=1KDS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KDS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kds]] is a 2 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=1KDS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1KDS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NPB:3-NITROPHENYLBORONIC+ACID'>NPB</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NPB:3-NITROPHENYLBORONIC+ACID'>NPB</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c3b\|1c3b]], [[1ga9\|1ga9]], [[3bls\|3bls]], [[1kdw\|1kdw]], [[1ke0\|1ke0]], [[1ke3\|1ke3]], [[1ke4\|1ke4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1c3b\|1c3b]], [[1ga9\|1ga9]], [[3bls\|3bls]], [[1kdw\|1kdw]], [[1ke0\|1ke0]], [[1ke3\|1ke3]], [[1ke4\|1ke4]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [http://pdbe.org/1kds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [http://www.ebi.ac.uk/pdbsum/1kds PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kds ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [http://pdbe.org/1kds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [http://www.ebi.ac.uk/pdbsum/1kds PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kds ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1kds" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kds" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 40:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Powers, R A]]		[[Category: Powers, R A]]
	[[Category: Shoichet, B K]]		[[Category: Shoichet, B K]]

OCA at 21:15, 24 January 2018

OCA — Wed, 24 Jan 2018 21:15:05 GMT

←Older revision		Revision as of 21:15, 24 January 2018
Line 1:		Line 1:
		+
	==X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 3-nitrophenylboronic acid==		==X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 3-nitrophenylboronic acid==
	<StructureSection load='1kds' size='340' side='right' caption='[[1kds]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1kds' size='340' side='right' caption='[[1kds]], [[Resolution\|resolution]] 2.15Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [http://pdbe.org/1kds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [http://www.ebi.ac.uk/pdbsum/1kds 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=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [http://pdbe.org/1kds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [http://www.ebi.ac.uk/pdbsum/1kds PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kds ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/1kds_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/1kds_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 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1kds" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kds" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Beta-lactamase\|Beta-lactamase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:09, 7 February 2016

OCA — Sun, 07 Feb 2016 04:09:34 GMT

←Older revision		Revision as of 04:09, 7 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kds ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:40, 9 September 2015

OCA — Wed, 09 Sep 2015 21:40:33 GMT

←Older revision		Revision as of 21:40, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1kds' size='340' side='right' caption='[[1kds]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='1kds' size='340' side='right' caption='[[1kds]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kds]] is a 2 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=1KDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kds]] is a 2 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=1KDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NPB:3-NITROPHENYLBORONIC+ACID'>NPB</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NPB:3-NITROPHENYLBORONIC+ACID'>NPB</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c3b\|1c3b]], [[1ga9\|1ga9]], [[3bls\|3bls]], [[1kdw\|1kdw]], [[1ke0\|1ke0]], [[1ke3\|1ke3]], [[1ke4\|1ke4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c3b\|1c3b]], [[1ga9\|1ga9]], [[3bls\|3bls]], [[1kdw\|1kdw]], [[1ke0\|1ke0]], [[1ke3\|1ke3]], [[1ke4\|1ke4]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [http://www.ebi.ac.uk/pdbsum/1kds 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=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [http://pdbe.org/1kds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [http://www.ebi.ac.uk/pdbsum/1kds PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1kds" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
-	[[Category: Escherichia coli]]
	[[Category: Powers, R A]]		[[Category: Powers, R A]]
	[[Category: Shoichet, B K]]		[[Category: Shoichet, B K]]

OCA at 07:44, 24 December 2014

OCA — Wed, 24 Dec 2014 07:44:58 GMT

←Older revision		Revision as of 07:44, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kds]] is a 2 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=1KDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kds]] is a 2 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=1KDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDS FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NPB:3-NITROPHENYLBORONIC+ACID'>NPB</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NPB:3-NITROPHENYLBORONIC+ACID'>NPB</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c3b\|1c3b]], [[1ga9\|1ga9]], [[3bls\|3bls]], [[1kdw\|1kdw]], [[1ke0\|1ke0]], [[1ke3\|1ke3]], [[1ke4\|1ke4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c3b\|1c3b]], [[1ga9\|1ga9]], [[3bls\|3bls]], [[1kdw\|1kdw]], [[1ke0\|1ke0]], [[1ke3\|1ke3]], [[1ke4\|1ke4]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [http://www.ebi.ac.uk/pdbsum/1kds 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=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [http://www.ebi.ac.uk/pdbsum/1kds PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI]] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Powers, R A.]]	+	[[Category: Powers, R A]]
-	[[Category: Shoichet, B K~~.]]~~	+	[[Category: Shoichet, B K]]
-	~~[[Category: Beta-lactamase~~]]	+
	[[Category: Cephalosporinase]]		[[Category: Cephalosporinase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Phenylboronic acid inhibitor complex]]		[[Category: Phenylboronic acid inhibitor complex]]
	[[Category: Serine hydrolase]]		[[Category: Serine hydrolase]]

OCA at 09:11, 28 September 2014

OCA — Sun, 28 Sep 2014 09:11:55 GMT

←Older revision		Revision as of 09:11, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1kds.~~png~~\|~~left~~\|200px]]	+	==X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 3-nitrophenylboronic acid==
		+	<StructureSection load='1kds' size='340' side='right' caption='[[1kds]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kds]] is a 2 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=1KDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDS FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NPB:3-NITROPHENYLBORONIC+ACID'>NPB</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c3b\|1c3b]], [[1ga9\|1ga9]], [[3bls\|3bls]], [[1kdw\|1kdw]], [[1ke0\|1ke0]], [[1ke3\|1ke3]], [[1ke4\|1ke4]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">K12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kds RCSB], [http://www.ebi.ac.uk/pdbsum/1kds 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/kd/1kds_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 ==
		+	Beta-lactamases are the most widespread resistance mechanism to beta-lactam antibiotics and are an increasing menace to public health. Several beta-lactamase structures have been determined, making this enzyme an attractive target for structure-based drug design. To facilitate inhibitor design for the class C beta-lactamase AmpC, binding site "hot spots" on the enzyme were identified using experimental and computational approaches. Experimentally, X-ray crystal structures of AmpC in complexes with four boronic acid inhibitors and a higher resolution (1.72 A) native apo structure were determined. Along with previously determined structures of AmpC in complexes with five other boronic acid inhibitors and four beta-lactams, consensus binding sites were identified. Computationally, the programs GRID, MCSS, and X-SITE were used to predict potential binding site hot spots on AmpC. Several consensus binding sites were identified from the crystal structures. An amide recognition site was identified by the interaction between the carbonyl oxygen in the R1 side chain of beta-lactams and the atom Ndelta2 of the conserved Asn152. Surprisingly, this site also recognizes the aryl rings of arylboronic acids, appearing to form quadrupole-dipole interactions with Asn152. The highly conserved "oxyanion" hole defines a site that recognizes both carbonyl and hydroxyl groups. A hydroxyl binding site was identified by the O2 hydroxyl in the boronic acids, which hydrogen bonds with Tyr150 and a conserved water. A hydrophobic site is formed by Leu119 and Leu293. A carboxylate binding site was identified by the ubiquitous C3(4) carboxylate of the beta-lactams, which interacts with Asn346 and Arg349. Four water sites were identified by ordered waters observed in most of the structures; these waters form extensive hydrogen-bonding networks with AmpC and occasionally the ligand. Predictions by the computational programs showed some correlation with the experimentally observed binding sites. Several sites were not predicted, but novel binding sites were suggested. Taken together, a map of binding site hot spots found on AmpC, along with information on the functionality recognized at each site, was constructed. This map may be useful for structure-based inhibitor design against AmpC.

-	~~{{STRUCTURE_1kds\| PDB=1kds \| SCENE= }}~~	+	Structure-based approach for binding site identification on AmpC beta-lactamase.,Powers RA, Shoichet BK J Med Chem. 2002 Jul 18;45(15):3222-34. PMID:12109906<ref>PMID:12109906</ref>

-	~~===X-ray crystal structure~~ of ~~AmpC beta-lactamase from E. coli in complex with~~ the ~~inhibitor 3-nitrophenylboronic acid===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12109906}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1kds]] is a 2 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=1KDS OCA].~~	+

	==See Also==		==See Also==
	*[[Beta-lactamase\|Beta-lactamase]]		*[[Beta-lactamase\|Beta-lactamase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012109906<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 05:32, 20 October 2012

OCA — Sat, 20 Oct 2012 05:32:43 GMT

←Older revision		Revision as of 05:32, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1kds]] is a 2 chain structure ~~of [[Beta-lactamase]]~~ 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=1KDS OCA].	+	[[1kds]] is a 2 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=1KDS OCA].

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

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

OCA — Wed, 25 Jul 2012 10:24:02 GMT

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

←Older revision

Revision as of 10:24, 25 July 2012

OCA at 10:24, 25 July 2012

OCA — Wed, 25 Jul 2012 10:24:01 GMT

←Older revision		Revision as of 10:24, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1kds.png\|left\|200px]]		[[Image:1kds.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1kds", 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_1kds\| PDB=1kds \| SCENE= }}		{{STRUCTURE_1kds\| PDB=1kds \| SCENE= }}

	===X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 3-nitrophenylboronic acid===		===X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 3-nitrophenylboronic acid===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12109906}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12109906 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12109906}}		{{ABSTRACT_PUBMED_12109906}}

	==About this Structure==		==About this Structure==
-	~~1KDS~~ is a 2 ~~chains~~ structure of ~~sequences~~ 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=1KDS OCA].	+	[[1kds]] is a 2 chain structure of [[Beta-lactamase]] 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=1KDS OCA].
		+
		+	==See Also==
		+	*[[Beta-lactamase\|Beta-lactamase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12109906~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012109906</ref><references group="xtra"/>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 30:		Line 21:
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Cephalosporinase]]		[[Category: Cephalosporinase]]
		+	[[Category: Hydrolase]]
	[[Category: Phenylboronic acid inhibitor complex]]		[[Category: Phenylboronic acid inhibitor complex]]
	[[Category: Serine hydrolase]]		[[Category: Serine hydrolase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:08:29 2009''