1kr3 - Revision history

OCA at 09:03, 16 August 2023

OCA — Wed, 16 Aug 2023 09:03:00 GMT

←Older revision		Revision as of 09:03, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1kr3' size='340' side='right'caption='[[1kr3]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1kr3' size='340' side='right'caption='[[1kr3]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kr3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacteroides_inaequalis"_eggerth_and_gagnon_1933 "bacteroides inaequalis" eggerth and gagnon 1933~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1KR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kr3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KR3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=113:7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC+ACID'>113</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1znb\|1znb]], [[1dd6\|1dd6]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=113:7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC+ACID'>113</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 "Bacteroides inaequalis" Eggerth and Gagnon 1933])</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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [https://pdbe.org/1kr3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [https://www.ebi.ac.uk/pdbsum/1kr3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kr3 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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [~~http~~://pdbe.org/1kr3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kr3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kr3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BLAB_BACFG BLAB_BACFG]] Can hydrolyze carbapenem compounds.	+	[https://www.uniprot.org/uniprot/BLAB_BACFG BLAB_BACFG] Can hydrolyze carbapenem compounds.
	== 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: Bacteroides ~~inaequalis eggerth and gagnon 1933]]~~	+	[[Category: Bacteroides fragilis]]
-	~~[[Category: Beta-lactamase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bateson~~, J H~~]]	+	[[Category: Bateson JH]]
-	[[Category: Boyd, H]]	+	[[Category: Boyd H]]
-	[[Category: Cheever, C]]	+	[[Category: Cheever C]]
-	[[Category: Concha~~, N O~~]]	+	[[Category: Concha NO]]
-	[[Category: Dez, E]]	+	[[Category: Dez E]]
-	~~[[Category: Fuente, J de la~~]]	+	[[Category: Gilpin M]]
-	[[Category: Gilpin, M]]	+	[[Category: Hueso-Rodrguez JA]]
-	[[Category: Hueso-Rodrguez~~, J A~~]]	+	[[Category: Janson CA]]
-	[[Category: Janson~~, C A~~]]	+	[[Category: Niconovich NL]]
-	[[Category: Niconovich~~, N L~~]]	+	[[Category: Payne DJ]]
-	[[Category: Payne~~, D J~~]]	+	[[Category: Pearson S]]
-	[[Category: Pearson, S]]	+	[[Category: Prez P]]
-	[[Category: Prez, P]]	+	[[Category: Rees M]]
-	[[Category: Rees, M]]	+	[[Category: Rittenhouse S]]
-	[[Category: Rittenhouse, S]]	+	[[Category: Rivera-Sagredo A]]
-	[[Category: Rivera-Sagredo, A]]	+	[[Category: Tew D]]
-	[[Category: Tew, D]]	+	[[Category: De la Fuente J]]
-	[[Category: ~~Beta sandwich]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metallo]]~~	+
-	~~[[Category: Protein-inhibitor complex~~]]	+

OCA at 07:48, 25 November 2020

OCA — Wed, 25 Nov 2020 07:48:56 GMT

←Older revision		Revision as of 07:48, 25 November 2020
Line 1:		Line 1:

	==Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.==		==Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.==
-	<StructureSection load='1kr3' size='340' side='right' caption='[[1kr3]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1kr3' size='340' side='right'caption='[[1kr3]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kr3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacteroides_inaequalis"_eggerth_and_gagnon_1933 "bacteroides inaequalis" eggerth and gagnon 1933]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kr3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacteroides_inaequalis"_eggerth_and_gagnon_1933 "bacteroides inaequalis" eggerth and gagnon 1933]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1KR3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=113:7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC+ACID'>113</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=113:7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC+ACID'>113</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1znb\|1znb]], [[1dd6\|1dd6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1znb\|1znb]], [[1dd6\|1dd6]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 "Bacteroides inaequalis" Eggerth and Gagnon 1933])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 "Bacteroides inaequalis" Eggerth and Gagnon 1933])</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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [http://pdbe.org/1kr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kr3 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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [http://pdbe.org/1kr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kr3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kr/1kr3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kr/1kr3_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 1kr3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kr3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 40:
	[[Category: Bacteroides inaequalis eggerth and gagnon 1933]]		[[Category: Bacteroides inaequalis eggerth and gagnon 1933]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Bateson, J H]]		[[Category: Bateson, J H]]
	[[Category: Boyd, H]]		[[Category: Boyd, H]]

OCA at 12:20, 12 October 2017

OCA — Thu, 12 Oct 2017 12:20:26 GMT

←Older revision		Revision as of 12:20, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.==		==Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.==
	<StructureSection load='1kr3' size='340' side='right' caption='[[1kr3]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1kr3' size='340' side='right' caption='[[1kr3]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 "Bacteroides inaequalis" Eggerth and Gagnon 1933])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 "Bacteroides inaequalis" Eggerth and Gagnon 1933])</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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [http://pdbe.org/1kr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kr3 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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [http://pdbe.org/1kr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kr3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kr3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1kr3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kr3" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Beta-lactamase\|Beta-lactamase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:44, 10 February 2016

OCA — Wed, 10 Feb 2016 05:44:15 GMT

←Older revision		Revision as of 05:44, 10 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=1kr3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:56, 11 September 2015

OCA — Fri, 11 Sep 2015 05:56:04 GMT

←Older revision		Revision as of 05:56, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1kr3' size='340' side='right' caption='[[1kr3]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1kr3' size='340' side='right' caption='[[1kr3]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kr3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacteroides_fragilis Bacteroides fragilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kr3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacteroides_inaequalis"_eggerth_and_gagnon_1933 "bacteroides inaequalis" eggerth and gagnon 1933]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KR3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=113:7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC+ACID'>113</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=113:7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC+ACID'>113</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1znb\|1znb]], [[1dd6\|1dd6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1znb\|1znb]], [[1dd6\|1dd6]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 Bacteroides ~~fragilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 "Bacteroides inaequalis" Eggerth and Gagnon 1933])</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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kr3 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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [http://pdbe.org/1kr3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kr3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~BLAB_BACFR BLAB_BACFR~~]] Can hydrolyze carbapenem compounds.	+	[[http://www.uniprot.org/uniprot/BLAB_BACFG BLAB_BACFG]] Can hydrolyze carbapenem compounds.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 1kr3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacteroides ~~fragilis~~]]	+	[[Category: Bacteroides inaequalis eggerth and gagnon 1933]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Bateson, J H]]		[[Category: Bateson, J H]]

OCA at 12:12, 25 December 2014

OCA — Thu, 25 Dec 2014 12:12:59 GMT

←Older revision		Revision as of 12:12, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kr3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KR3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kr3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KR3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=113:7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC+ACID'>113</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=113:7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC+ACID'>113</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1znb\|1znb]], [[1dd6\|1dd6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1znb\|1znb]], [[1dd6\|1dd6]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 Bacteroides fragilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 Bacteroides fragilis])</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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kr3 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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kr3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BLAB_BACFR BLAB_BACFR]] Can hydrolyze carbapenem compounds.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Bacteroides fragilis]]		[[Category: Bacteroides fragilis]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
-	[[Category: Bateson, J H.]]	+	[[Category: Bateson, J H]]
-	[[Category: Boyd, H.]]	+	[[Category: Boyd, H]]
-	[[Category: Cheever, C.]]	+	[[Category: Cheever, C]]
-	[[Category: Concha, N O.]]	+	[[Category: Concha, N O]]
-	[[Category: Dez, E.]]	+	[[Category: Dez, E]]
-	[[Category: Fuente, J de la.]]	+	[[Category: Fuente, J de la]]
-	[[Category: Gilpin, M.]]	+	[[Category: Gilpin, M]]
-	[[Category: Hueso-Rodrguez, J A.]]	+	[[Category: Hueso-Rodrguez, J A]]
-	[[Category: Janson, C A.]]	+	[[Category: Janson, C A]]
-	[[Category: Niconovich, N L.]]	+	[[Category: Niconovich, N L]]
-	[[Category: Payne, D J.]]	+	[[Category: Payne, D J]]
-	[[Category: Pearson, S.]]	+	[[Category: Pearson, S]]
-	[[Category: Prez, P.]]	+	[[Category: Prez, P]]
-	[[Category: Rees, M.]]	+	[[Category: Rees, M]]
-	[[Category: Rittenhouse, S.]]	+	[[Category: Rittenhouse, S]]
-	[[Category: Rivera-Sagredo, A.]]	+	[[Category: Rivera-Sagredo, A]]
-	[[Category: Tew, D.]]	+	[[Category: Tew, D]]
	[[Category: Beta sandwich]]		[[Category: Beta sandwich]]
-	[[Category: Beta-lactamase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Metallo]]		[[Category: Metallo]]
	[[Category: Protein-inhibitor complex]]		[[Category: Protein-inhibitor complex]]

OCA at 14:11, 28 September 2014

OCA — Sun, 28 Sep 2014 14:11:11 GMT

←Older revision		Revision as of 14:11, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1kr3.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.==
		+	<StructureSection load='1kr3' size='340' side='right' caption='[[1kr3]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kr3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KR3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=113:7,8-DIHYDROXY-1-METHOXY-3-METHYL-10-OXO-4,10-DIHYDRO-1H,3H-PYRANO[4,3-B]CHROMENE-9-CARBOXYLIC+ACID'>113</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1znb\|1znb]], [[1dd6\|1dd6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CfiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 Bacteroides fragilis])</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=1kr3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kr3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kr3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kr3 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/kr/1kr3_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 ==
		+	This work describes the discovery and characterization of a novel series of tricyclic natural product-derived metallo-beta-lactamase inhibitors. Natural product screening of the Bacillus cereus II enzyme identified an extract from a strain of Chaetomium funicola with inhibitory activity against metallo-beta-lactamases. SB236050, SB238569, and SB236049 were successfully extracted and purified from this extract. The most active of these compounds was SB238569, which possessed K(i) values of 79, 17, and 3.4 microM for the Bacillus cereus II, Pseudomonas aeruginosa IMP-1, and Bacteroides fragilis CfiA metallo-beta-lactamases, respectively, yet none of the compounds exhibited any inhibitory activity against the Stenotrophomonas maltophilia L-1 metallo-beta-lactamase (50% inhibitory concentration > 1,000 microM). The lack of activity against angiotensin-converting enzyme and serine beta-lactamases demonstrated the selective nature of these compounds. The crystal structure of SB236050 complexed in the active site of CfiA has been obtained to a resolution of 2.5 A. SB236050 exhibits key polar interactions with Lys184, Asn193, and His162 and a stacking interaction with the indole ring of Trp49 in the flap, which is in the closed conformation over the active site groove. SB236050 and SB238569 also demonstrate good antibacterial synergy with meropenem. Eight micrograms of SB236050 per ml gave rise to an eightfold drop in the MIC of meropenem for two clinical isolates of B. fragilis producing CfiA, making these strains sensitive to meropenem (MIC < or = 4 microg/ml). Consequently, this series of metallo-beta-lactamase inhibitors exhibit the most promising antibacterial synergy activity so far observed against organisms producing metallo-beta-lactamases.

-	~~{{STRUCTURE_1kr3\| PDB=1kr3 \| SCENE= }}~~	+	Identification of a series of tricyclic natural products as potent broad-spectrum inhibitors of metallo-beta-lactamases.,Payne DJ, Hueso-Rodriguez JA, Boyd H, Concha NO, Janson CA, Gilpin M, Bateson JH, Cheever C, Niconovich NL, Pearson S, Rittenhouse S, Tew D, Diez E, Perez P, De La Fuente J, Rees M, Rivera-Sagredo A Antimicrob Agents Chemother. 2002 Jun;46(6):1880-6. PMID:12019104<ref>PMID:12019104</ref>

-	~~===Crystal Structure~~ of the ~~Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12019104}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1kr3]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA].~~	+

	==See Also==		==See Also==
	*[[Beta-lactamase\|Beta-lactamase]]		*[[Beta-lactamase\|Beta-lactamase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012019104<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacteroides fragilis]]		[[Category: Bacteroides fragilis]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]

OCA at 16:31, 20 October 2012

OCA — Sat, 20 Oct 2012 16:31:49 GMT

←Older revision		Revision as of 16:31, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1kr3]] is a 2 chain structure ~~of [[Beta-lactamase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA].	+	[[1kr3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA].

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

OCA: Protected "1kr3" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 21:58:24 GMT

Protected "1kr3" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:58, 26 July 2012

OCA at 21:58, 26 July 2012

OCA — Thu, 26 Jul 2012 21:58:21 GMT

←Older revision		Revision as of 21:58, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1kr3.png\|left\|200px]]		[[Image:1kr3.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1kr3", 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_1kr3\| PDB=1kr3 \| SCENE= }}		{{STRUCTURE_1kr3\| PDB=1kr3 \| SCENE= }}

	===Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.===		===Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12019104}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12019104 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12019104}}		{{ABSTRACT_PUBMED_12019104}}

	==About this Structure==		==About this Structure==
-	~~1KR3~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA].	+	[[1kr3]] is a 2 chain structure of [[Beta-lactamase]] with sequence from [http://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KR3 OCA].
		+
		+	==See Also==
		+	*[[Beta-lactamase\|Beta-lactamase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12019104~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012019104</ref><references group="xtra"/>
	[[Category: Bacteroides fragilis]]		[[Category: Bacteroides fragilis]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
Line 45:		Line 36:
	[[Category: Beta sandwich]]		[[Category: Beta sandwich]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Hydrolase]]
	[[Category: Metallo]]		[[Category: Metallo]]
	[[Category: Protein-inhibitor complex]]		[[Category: Protein-inhibitor complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:53:11 2009''