2r9w - Revision history

OCA at 11:51, 30 August 2023

OCA — Wed, 30 Aug 2023 11:51:02 GMT

←Older revision		Revision as of 11:51, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2r9w' size='340' side='right'caption='[[2r9w]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2r9w' size='340' side='right'caption='[[2r9w]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r9w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R9W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r9w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R9W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=23C:2-[(1R)-1-CARBOXY-2-NAPHTHALEN-1-YLETHYL]-1,3-DIOXO-2,3-DIHYDRO-1H-ISOINDOLE-5-CARBOXYLIC+ACID'>23C</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pu2\|2pu2]], [[2r9x\|2r9x]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=23C:2-[(1R)-1-CARBOXY-2-NAPHTHALEN-1-YLETHYL]-1,3-DIOXO-2,3-DIHYDRO-1H-ISOINDOLE-5-CARBOXYLIC+ACID'>23C</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [https://pdbe.org/2r9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [https://www.ebi.ac.uk/pdbsum/2r9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r9w 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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [https://pdbe.org/2r9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [https://www.ebi.ac.uk/pdbsum/2r9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r9w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://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]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta~~-~~lactamase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Babaoglu, K]]	+	[[Category: Babaoglu K]]
-	[[Category: Shoichet~~, B K]]~~	+	[[Category: Shoichet BK]]
-	~~[[Category: Ampc beta lactamase]]~~	+
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pthalamide~~]]	+

OCA at 04:19, 2 July 2021

OCA — Fri, 02 Jul 2021 04:19:20 GMT

←Older revision		Revision as of 04:19, 2 July 2021
Line 1:		Line 1:

	==AmpC beta-lactamase with bound Phthalamide inhibitor==		==AmpC beta-lactamase with bound Phthalamide inhibitor==
-	<StructureSection load='2r9w' size='340' side='right' caption='[[2r9w]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2r9w' size='340' side='right'caption='[[2r9w]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r9w]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R9W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2R9W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r9w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R9W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=23C:2-[(1R)-1-CARBOXY-2-NAPHTHALEN-1-YLETHYL]-1,3-DIOXO-2,3-DIHYDRO-1H-ISOINDOLE-5-CARBOXYLIC+ACID'>23C</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=23C:2-[(1R)-1-CARBOXY-2-NAPHTHALEN-1-YLETHYL]-1,3-DIOXO-2,3-DIHYDRO-1H-ISOINDOLE-5-CARBOXYLIC+ACID'>23C</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pu2\|2pu2]], [[2r9x\|2r9x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pu2\|2pu2]], [[2r9x\|2r9x]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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'>[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [~~http~~://pdbe.org/2r9w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2r9w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2r9w 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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [https://pdbe.org/2r9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [https://www.ebi.ac.uk/pdbsum/2r9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r9w 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]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r9/2r9w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r9/2r9w_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 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2r9w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2r9w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 40:
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Babaoglu, K]]		[[Category: Babaoglu, K]]
	[[Category: Shoichet, B K]]		[[Category: Shoichet, B K]]

OCA at 07:46, 25 October 2017

OCA — Wed, 25 Oct 2017 07:46:32 GMT

←Older revision		Revision as of 07:46, 25 October 2017
Line 1:		Line 1:
		+
	==AmpC beta-lactamase with bound Phthalamide inhibitor==		==AmpC beta-lactamase with bound Phthalamide inhibitor==
	<StructureSection load='2r9w' size='340' side='right' caption='[[2r9w]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2r9w' size='340' side='right' caption='[[2r9w]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [http://pdbe.org/2r9w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [http://www.ebi.ac.uk/pdbsum/2r9w 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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [http://pdbe.org/2r9w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [http://www.ebi.ac.uk/pdbsum/2r9w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r9w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2r9w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2r9w" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Beta-lactamase\|Beta-lactamase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:56, 8 February 2016

OCA — Mon, 08 Feb 2016 03:56:16 GMT

←Older revision		Revision as of 03:56, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='2r9w' size='340' side='right' caption='[[2r9w]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2r9w' size='340' side='right' caption='[[2r9w]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r9w]] 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=2R9W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R9W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r9w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R9W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R9W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=23C:2-[(1R)-1-CARBOXY-2-NAPHTHALEN-1-YLETHYL]-1,3-DIOXO-2,3-DIHYDRO-1H-ISOINDOLE-5-CARBOXYLIC+ACID'>23C</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=23C:2-[(1R)-1-CARBOXY-2-NAPHTHALEN-1-YLETHYL]-1,3-DIOXO-2,3-DIHYDRO-1H-ISOINDOLE-5-CARBOXYLIC+ACID'>23C</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pu2\|2pu2]], [[2r9x\|2r9x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pu2\|2pu2]], [[2r9x\|2r9x]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA ([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">ampC, ampA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [http://www.ebi.ac.uk/pdbsum/2r9w 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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [http://pdbe.org/2r9w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [http://www.ebi.ac.uk/pdbsum/2r9w PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2r9w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2r9w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Babaoglu, K]]		[[Category: Babaoglu, K]]
	[[Category: Shoichet, B K]]		[[Category: Shoichet, B K]]

OCA at 20:25, 24 December 2014

OCA — Wed, 24 Dec 2014 20:25:01 GMT

←Older revision		Revision as of 20:25, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r9w]] 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=2R9W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R9W FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r9w]] 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=2R9W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R9W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=23C:2-[(1R)-1-CARBOXY-2-NAPHTHALEN-1-YLETHYL]-1,3-DIOXO-2,3-DIHYDRO-1H-ISOINDOLE-5-CARBOXYLIC+ACID'>23C</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=23C:2-[(1R)-1-CARBOXY-2-NAPHTHALEN-1-YLETHYL]-1,3-DIOXO-2,3-DIHYDRO-1H-ISOINDOLE-5-CARBOXYLIC+ACID'>23C</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pu2\|2pu2]], [[2r9x\|2r9x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pu2\|2pu2]], [[2r9x\|2r9x]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA ([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">ampC, ampA ([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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [http://www.ebi.ac.uk/pdbsum/2r9w 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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [http://www.ebi.ac.uk/pdbsum/2r9w 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: Babaoglu, K.]]	+	[[Category: Babaoglu, K]]
-	[[Category: Shoichet, B K.]]	+	[[Category: Shoichet, B K]]
	[[Category: Ampc beta lactamase]]		[[Category: Ampc beta lactamase]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Pthalamide]]		[[Category: Pthalamide]]

OCA at 07:30, 29 September 2014

OCA — Mon, 29 Sep 2014 07:30:02 GMT

←Older revision		Revision as of 07:30, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2r9w.~~png~~\|~~left~~\|200px]]	+	==AmpC beta-lactamase with bound Phthalamide inhibitor==
		+	<StructureSection load='2r9w' size='340' side='right' caption='[[2r9w]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2r9w]] 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=2R9W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R9W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=23C:2-[(1R)-1-CARBOXY-2-NAPHTHALEN-1-YLETHYL]-1,3-DIOXO-2,3-DIHYDRO-1H-ISOINDOLE-5-CARBOXYLIC+ACID'>23C</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2pu2\|2pu2]], [[2r9x\|2r9x]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA ([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=2r9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r9w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r9w RCSB], [http://www.ebi.ac.uk/pdbsum/2r9w 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/r9/2r9w_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 ==
		+	High-throughput screening (HTS) is widely used in drug discovery. Especially for screens of unbiased libraries, false positives can dominate "hit lists"; their origins are much debated. Here we determine the mechanism of every active hit from a screen of 70,563 unbiased molecules against beta-lactamase using quantitative HTS (qHTS). Of the 1274 initial inhibitors, 95% were detergent-sensitive and were classified as aggregators. Among the 70 remaining were 25 potent, covalent-acting beta-lactams. Mass spectra, counter-screens, and crystallography identified 12 as promiscuous covalent inhibitors. The remaining 33 were either aggregators or irreproducible. No specific reversible inhibitors were found. We turned to molecular docking to prioritize molecules from the same library for testing at higher concentrations. Of 16 tested, 2 were modest inhibitors. Subsequent X-ray structures corresponded to the docking prediction. Analog synthesis improved affinity to 8 microM. These results suggest that it may be the physical behavior of organic molecules, not their reactivity, that accounts for most screening artifacts. Structure-based methods may prioritize weak-but-novel chemotypes in unbiased library screens.

-	~~{{STRUCTURE_2r9w\| PDB=2r9w \| SCENE= }}~~	+	Comprehensive Mechanistic Analysis of Hits from High-Throughput and Docking Screens against beta-Lactamase.,Babaoglu K, Simeonov A, Irwin JJ, Nelson ME, Feng B, Thomas CJ, Cancian L, Costi MP, Maltby DA, Jadhav A, Inglese J, Austin CP, Shoichet BK J Med Chem. 2008 Mar 12;. PMID:18333608<ref>PMID:18333608</ref>

-	~~===AmpC beta-lactamase with bound Phthalamide inhibitor===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18333608}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2r9w]] 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=2R9W OCA].~~	+

	==See Also==		==See Also==
	*[[Beta-lactamase\|Beta-lactamase]]		*[[Beta-lactamase\|Beta-lactamase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018333608<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 08:49, 20 October 2012

OCA — Sat, 20 Oct 2012 08:49:26 GMT

←Older revision		Revision as of 08:49, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2r9w]] 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=2R9W OCA].	+	[[2r9w]] 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=2R9W OCA].

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

OCA: Protected "2r9w" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 20:52:42 GMT

Protected "2r9w" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:52, 25 July 2012

OCA at 20:52, 25 July 2012

OCA — Wed, 25 Jul 2012 20:52:41 GMT

←Older revision		Revision as of 20:52, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2r9w.png\|left\|200px]]		[[Image:2r9w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2r9w", 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_2r9w\| PDB=2r9w \| SCENE= }}		{{STRUCTURE_2r9w\| PDB=2r9w \| SCENE= }}

	===AmpC beta-lactamase with bound Phthalamide inhibitor===		===AmpC beta-lactamase with bound Phthalamide inhibitor===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18333608}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18333608 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18333608}}		{{ABSTRACT_PUBMED_18333608}}

	==About this Structure==		==About this Structure==
-	~~2R9W~~ 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=2R9W OCA].	+	[[2r9w]] 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=2R9W OCA].
		+
		+	==See Also==
		+	*[[Beta-lactamase\|Beta-lactamase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18333608~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018333608</ref><references group="xtra"/>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 31:		Line 22:
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	[[Category: Periplasm]]
	[[Category: Pthalamide]]		[[Category: Pthalamide]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:37:56 2009''

OCA at 16:37, 16 February 2009

OCA — Mon, 16 Feb 2009 16:37:58 GMT

←Older revision		Revision as of 16:37, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2R9W 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=2R9W OCA].	+	2R9W 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=2R9W OCA].

	==Reference==		==Reference==
-	Comprehensive Mechanistic Analysis of Hits from High-Throughput and Docking Screens against beta-Lactamase., Babaoglu K, Simeonov A, Irwin JJ, Nelson ME, Feng B, Thomas CJ, Cancian L, Costi MP, Maltby DA, Jadhav A, Inglese J, Austin CP, Shoichet BK, J Med Chem. 2008 Mar 12;. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18333608 18333608]~~	+	<ref group="xtra">PMID:18333608</ref><references group="xtra"/>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Babaoglu, K.]]		[[Category: Babaoglu, K.]]
	[[Category: Shoichet, B K.]]		[[Category: Shoichet, B K.]]
Line 35:		Line 34:
	[[Category: Pthalamide]]		[[Category: Pthalamide]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 22~~:52:~~39 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:37:56 2009''