5kzh - Revision history

OCA at 16:03, 4 October 2023

OCA — Wed, 04 Oct 2023 16:03:17 GMT

←Older revision		Revision as of 16:03, 4 October 2023
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	<StructureSection load='5kzh' size='340' side='right'caption='[[5kzh]], [[Resolution\|resolution]] 1.61Å' scene=''>		<StructureSection load='5kzh' size='340' side='right'caption='[[5kzh]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kzh]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aciba Aciba~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KZH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KZH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kzh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KZH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KZH FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'>ACT</scene~~>, ~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 1.61Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~KCX~~:~~LYSINE~~+~~NZ-CARBOXYLIC+ACID~~'>~~KCX~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">oxa-51~~, ~~blaOXA-51, AQ480_08190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])~~<~~/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=5kzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kzh OCA], [https://pdbe.org/5kzh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kzh RCSB], [https://www.ebi.ac.uk/pdbsum/5kzh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kzh 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5kzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kzh OCA], [~~http~~://pdbe.org/5kzh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kzh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kzh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kzh ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5QT35_ACIBA Q5QT35_ACIBA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aciba]]~~	+	[[Category: Acinetobacter baumannii]]
-	~~[[Category: Beta-lactamase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: June~~, C M~~]]	+	[[Category: June CM]]
-	[[Category: Leonard~~, D A~~]]	+	[[Category: Leonard DA]]
-	[[Category: Powers~~, R A]]~~	+	[[Category: Powers RA]]
-	~~[[Category: Antibiotic]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 16:30, 11 December 2019

OCA — Wed, 11 Dec 2019 16:30:44 GMT

←Older revision		Revision as of 16:30, 11 December 2019
Line 1:		Line 1:

	==High Resolution Structure of Acinetobacter baumannii beta-lactamase OXA-51==		==High Resolution Structure of Acinetobacter baumannii beta-lactamase OXA-51==
-	<StructureSection load='5kzh' size='340' side='right' caption='[[5kzh]], [[Resolution\|resolution]] 1.61Å' scene=''>	+	<StructureSection load='5kzh' size='340' side='right'caption='[[5kzh]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kzh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KZH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KZH FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kzh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KZH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KZH FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5kzh" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kzh" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	[[Category: Aciba]]		[[Category: Aciba]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: June, C M]]		[[Category: June, C M]]
	[[Category: Leonard, D A]]		[[Category: Leonard, D A]]

OCA at 13:05, 6 November 2017

OCA — Mon, 06 Nov 2017 13:05:36 GMT

←Older revision		Revision as of 13:05, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5kzh' size='340' side='right' caption='[[5kzh]], [[Resolution\|resolution]] 1.61Å' scene=''>		<StructureSection load='5kzh' size='340' side='right' caption='[[5kzh]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kzh]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KZH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KZH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kzh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciba Aciba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KZH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KZH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxa-51, blaOXA-51, AQ480_08190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=470 ACIBA])</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=5kzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kzh OCA], [http://pdbe.org/5kzh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kzh RCSB], [http://www.ebi.ac.uk/pdbsum/5kzh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kzh ProSAT]</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=5kzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kzh OCA], [http://pdbe.org/5kzh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kzh RCSB], [http://www.ebi.ac.uk/pdbsum/5kzh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kzh ProSAT]</span></td></tr>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aciba]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: June, C M]]		[[Category: June, C M]]

OCA at 13:56, 5 October 2016

OCA — Wed, 05 Oct 2016 13:56:03 GMT

←Older revision		Revision as of 13:56, 5 October 2016
Line 9:		Line 9:
	<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=5kzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kzh OCA], [http://pdbe.org/5kzh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kzh RCSB], [http://www.ebi.ac.uk/pdbsum/5kzh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kzh ProSAT]</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=5kzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kzh OCA], [http://pdbe.org/5kzh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kzh RCSB], [http://www.ebi.ac.uk/pdbsum/5kzh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kzh ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	OXA-51 is a class D beta-lactamase that is thought to be the native carbapenemase of Acinetobacter baumannii. Many variants of OXA-51 containing active site substitutions have been identified from A. baumannii isolates, and some of these substitutions increase hydrolytic activity toward carbapenem antibiotics. We have determined the high-resolution structures of apo OXA-51 and OXA-51 with one such substitution (I129L) with the carbapenem doripenem trapped in the active site as an acyl-intermediate. The structure shows that acyl-doripenem adopts an orientation very similar to carbapenem ligands observed in the active site of OXA-24/40 (doripenem) and OXA-23 (meropenem). In the OXA-51 variant/doripenem complex, the indole ring of W222 is oriented away from the doripenem binding site, thereby eliminating a clash that is predicted to occur in wildtype OXA-51. Similarly, in the OXA-51 variant complex, L129 adopts a different rotamer compared to I129 in wildtype OXA-51. This alternative position moves its side chain away from the hydroxyethyl moiety of doripenem and relieves another potential clash between the enzyme and carbapenem substrates. Molecular dynamics simulations of OXA-51 and OXA-51 I129L demonstrate that compared to isoleucine, a leucine at this position greatly favors a rotamer that accommodates the ligand. These results provide a molecular justification for how this substitution generates enhanced binding affinity for carbapenems, and therefore helps explain the prevalence of this substitution in clinical OXA-51 variants.
		+
		+	The structure of a doripenem-bound OXA-51 class D beta-lactamase variant with enhanced carbapenemase activity.,June CM, Muckenthaler TJ, Schroder EC, Klamer ZL, Wawrzak Z, Powers RA, Szarecka A, Leonard DA Protein Sci. 2016 Sep 16. doi: 10.1002/pro.3040. PMID:27636561<ref>PMID:27636561</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kzh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 00:07, 10 September 2016

OCA — Sat, 10 Sep 2016 00:07:51 GMT

←Older revision		Revision as of 00:07, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kzh is ~~ON HOLD until Paper Publication~~	+	==High Resolution Structure of Acinetobacter baumannii beta-lactamase OXA-51==
-		+	<StructureSection load='5kzh' size='340' side='right' caption='[[5kzh]], [[Resolution\|resolution]] 1.61Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kzh]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KZH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KZH FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></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=5kzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kzh OCA], [http://pdbe.org/5kzh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kzh RCSB], [http://www.ebi.ac.uk/pdbsum/5kzh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kzh ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: June, C M]]
		+	[[Category: Leonard, D A]]
		+	[[Category: Powers, R A]]
		+	[[Category: Antibiotic]]
		+	[[Category: Hydrolase]]

OCA: Protected "5kzh" [edit=sysop:move=sysop]

OCA — Thu, 04 Aug 2016 02:14:22 GMT

Protected "5kzh" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:14, 4 August 2016

OCA: New page: '''Unreleased structure''' The entry 5kzh is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Thu, 04 Aug 2016 02:14:21 GMT

New page: '''Unreleased structure''' The entry 5kzh is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5kzh is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]