2hdr - Revision history

OCA at 09:56, 30 August 2023

2023-08-30T09:56:04Z

←Older revision		Revision as of 09:56, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2hdr' size='340' side='right'caption='[[2hdr]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2hdr' size='340' side='right'caption='[[2hdr]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hdr]] 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=2HDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hdr]] 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=2HDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HDR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=4A3:4~~-~~AMINO-3-HYDROXYBENZOIC+ACID'>4A3</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2hdq\|2hdq]], [[2hds\|2hds]], [[2hdu\|2hdu]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4A3:4-AMINO-3-HYDROXYBENZOIC+ACID'>4A3</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 ([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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [https://pdbe.org/2hdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [https://www.ebi.ac.uk/pdbsum/2hdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hdr 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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [https://pdbe.org/2hdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [https://www.ebi.ac.uk/pdbsum/2hdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hdr 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 fragment-based drug design beta-lactamase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:37, 17 March 2021

2021-03-17T07:37:16Z

←Older revision		Revision as of 07:37, 17 March 2021
Line 1:		Line 1:

	==AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid==		==AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid==
-	<StructureSection load='2hdr' size='340' side='right' caption='[[2hdr]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2hdr' size='340' side='right'caption='[[2hdr]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hdr]] 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=2HDR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2HDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hdr]] 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=2HDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HDR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4A3:4-AMINO-3-HYDROXYBENZOIC+ACID'>4A3</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=4A3:4-AMINO-3-HYDROXYBENZOIC+ACID'>4A3</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">[[2hdq\|2hdq]], [[2hds\|2hds]], [[2hdu\|2hdu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2hdq\|2hdq]], [[2hds\|2hds]], [[2hdu\|2hdu]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC ([~~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 ([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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [~~http~~://pdbe.org/2hdr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2hdr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2hdr 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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [https://pdbe.org/2hdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [https://www.ebi.ac.uk/pdbsum/2hdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hdr 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/hd/2hdr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hd/2hdr_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 2hdr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2hdr" 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]]
	[[Category: Ampc fragment-based drug design beta-lactamase]]		[[Category: Ampc fragment-based drug design beta-lactamase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:10, 18 October 2017

2017-10-18T08:10:57Z

←Older revision		Revision as of 08:10, 18 October 2017
Line 1:		Line 1:
		+
	==AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid==		==AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid==
	<StructureSection load='2hdr' size='340' side='right' caption='[[2hdr]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2hdr' size='340' side='right' caption='[[2hdr]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC ([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 ([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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [http://pdbe.org/2hdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [http://www.ebi.ac.uk/pdbsum/2hdr 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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [http://pdbe.org/2hdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [http://www.ebi.ac.uk/pdbsum/2hdr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hdr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2hdr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2hdr" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Beta-lactamase\|Beta-lactamase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:40, 9 February 2016

2016-02-09T11:40:02Z

←Older revision		Revision as of 11:40, 9 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=2hdr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:51, 10 September 2015

2015-09-10T21:51:41Z

←Older revision		Revision as of 21:51, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2hdr' size='340' side='right' caption='[[2hdr]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2hdr' size='340' side='right' caption='[[2hdr]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hdr]] is a 2 chain structure with sequence from [http://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=2HDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hdr]] 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=2HDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HDR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4A3:4-AMINO-3-HYDROXYBENZOIC+ACID'>4A3</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=4A3:4-AMINO-3-HYDROXYBENZOIC+ACID'>4A3</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">[[2hdq\|2hdq]], [[2hds\|2hds]], [[2hdu\|2hdu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hdq\|2hdq]], [[2hds\|2hds]], [[2hdu\|2hdu]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC ([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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [http://www.ebi.ac.uk/pdbsum/2hdr 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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [http://pdbe.org/2hdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [http://www.ebi.ac.uk/pdbsum/2hdr 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 2hdr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Babaoglu, K]]		[[Category: Babaoglu, K]]
	[[Category: Shoichet, B K]]		[[Category: Shoichet, B K]]
	[[Category: Ampc fragment-based drug design beta-lactamase]]		[[Category: Ampc fragment-based drug design beta-lactamase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 06:33, 25 December 2014

2014-12-25T06:33:33Z

←Older revision		Revision as of 06:33, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hdr]] is a 2 chain structure with sequence from [http://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=2HDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HDR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hdr]] is a 2 chain structure with sequence from [http://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=2HDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HDR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4A3:4-AMINO-3-HYDROXYBENZOIC+ACID'>4A3</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=4A3:4-AMINO-3-HYDROXYBENZOIC+ACID'>4A3</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hdq\|2hdq]], [[2hds\|2hds]], [[2hdu\|2hdu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hdq\|2hdq]], [[2hds\|2hds]], [[2hdu\|2hdu]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [http://www.ebi.ac.uk/pdbsum/2hdr 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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [http://www.ebi.ac.uk/pdbsum/2hdr 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 k-12]]		[[Category: Escherichia coli k-12]]
-	[[Category: Babaoglu, K.]]	+	[[Category: Babaoglu, K]]
-	[[Category: Shoichet, B K.]]	+	[[Category: Shoichet, B K]]
	[[Category: Ampc fragment-based drug design beta-lactamase]]		[[Category: Ampc fragment-based drug design beta-lactamase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 10:00, 29 September 2014

2014-09-29T10:00:40Z

←Older revision		Revision as of 10:00, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2hdr.~~png~~\|~~left~~\|200px]]	+	==AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid==
		+	<StructureSection load='2hdr' size='340' side='right' caption='[[2hdr]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2hdr]] is a 2 chain structure with sequence from [http://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=2HDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HDR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4A3:4-AMINO-3-HYDROXYBENZOIC+ACID'>4A3</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hdq\|2hdq]], [[2hds\|2hds]], [[2hdu\|2hdu]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=2hdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hdr RCSB], [http://www.ebi.ac.uk/pdbsum/2hdr 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/hd/2hdr_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 ==
		+	Fragment-based screens test multiple low-molecular weight molecules for binding to a target. Fragments often bind with low affinities but typically have better ligand efficiencies (DeltaG(bind)/heavy atom count) than traditional screening hits. This efficiency, combined with accompanying atomic-resolution structures, has made fragments popular starting points for drug discovery programs. Fragment-based design adopts a constructive strategy: affinity is enhanced either by cycles of functional-group addition or by joining two independent fragments together. The final inhibitor is expected to adopt the same geometry as the original fragment hit. Here we consider whether the inverse, deconstructive logic also applies--can one always parse a higher-affinity inhibitor into fragments that recapitulate the binding geometry of the larger molecule? Cocrystal structures of fragments deconstructed from a known beta-lactamase inhibitor suggest that this is not always the case.

-	~~{{STRUCTURE_2hdr\| PDB=2hdr \| SCENE= }}~~	+	Deconstructing fragment-based inhibitor discovery.,Babaoglu K, Shoichet BK Nat Chem Biol. 2006 Dec;2(12):720-3. Epub 2006 Oct 29. PMID:17072304<ref>PMID:17072304</ref>

-	~~===AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17072304}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2hdr]] is~~ a ~~2 chain structure with sequence from [http://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=2HDR OCA].~~	+

	==See Also==		==See Also==
	*[[Beta-lactamase\|Beta-lactamase]]		*[[Beta-lactamase\|Beta-lactamase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017072304<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]

OCA at 13:43, 20 October 2012

2012-10-20T13:43:19Z

←Older revision		Revision as of 13:43, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2hdr]] is a 2 chain structure ~~of [[Beta-lactamase]]~~ with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k12~~ Escherichia coli ~~k12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HDR OCA].	+	[[2hdr]] is a 2 chain structure with sequence from [http://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=2HDR OCA].

	==See Also==		==See Also==
Line 16:		Line 16:
	<ref group="xtra">PMID:017072304</ref><references group="xtra"/>		<ref group="xtra">PMID:017072304</ref><references group="xtra"/>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
-	[[Category: Escherichia coli ~~k12~~]]	+	[[Category: Escherichia coli k-12]]
	[[Category: Babaoglu, K.]]		[[Category: Babaoglu, K.]]
	[[Category: Shoichet, B K.]]		[[Category: Shoichet, B K.]]
	[[Category: Ampc fragment-based drug design beta-lactamase]]		[[Category: Ampc fragment-based drug design beta-lactamase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

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

2012-07-26T12:53:15Z

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

←Older revision

Revision as of 12:53, 26 July 2012

OCA at 12:53, 26 July 2012

2012-07-26T12:53:14Z

←Older revision		Revision as of 12:53, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2hdr.png\|left\|200px]]		[[Image:2hdr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2hdr", 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_2hdr\| PDB=2hdr \| SCENE= }}		{{STRUCTURE_2hdr\| PDB=2hdr \| SCENE= }}

	===AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid===		===AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17072304}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17072304 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17072304}}		{{ABSTRACT_PUBMED_17072304}}

	==About this Structure==		==About this Structure==
-	~~2HDR~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HDR OCA].	+	[[2hdr]] is a 2 chain structure of [[Beta-lactamase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HDR OCA].
		+
		+	==See Also==
		+	*[[Beta-lactamase\|Beta-lactamase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17072304~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017072304</ref><references group="xtra"/>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Escherichia coli k12]]		[[Category: Escherichia coli k12]]
Line 29:		Line 20:
	[[Category: Shoichet, B K.]]		[[Category: Shoichet, B K.]]
	[[Category: Ampc fragment-based drug design beta-lactamase]]		[[Category: Ampc fragment-based drug design beta-lactamase]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 09:29:19 2009''~~	+