OCA at 09:28, 26 May 2021

OCA — Wed, 26 May 2021 09:28:49 GMT

←Older revision		Revision as of 09:28, 26 May 2021
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	==avibactam-CDD-1 2 minute complex==		==avibactam-CDD-1 2 minute complex==
-	<StructureSection load='7kep' size='340' side='right'caption='[[7kep]]' scene=''>	+	<StructureSection load='7kep' size='340' side='right'caption='[[7kep]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KEP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7KEP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kep]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_difficilis"_hall_and_o'toole_1935 "bacillus difficilis" hall and o'toole 1935]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KEP FirstGlance]. <br>
-	</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=7kep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kep OCA], [~~http~~://pdbe.org/7kep PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7kep RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7kep PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7kep ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FYG:(2S,5R)-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]octane-2-carboxamide'>FYG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">blaR1_4, blaR1_1, E5F39_11445, SAMEA2239407_03320, SAMEA3374989_01677 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1496 "Bacillus difficilis" Hall and O'Toole 1935])</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=7kep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kep OCA], [https://pdbe.org/7kep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kep RCSB], [https://www.ebi.ac.uk/pdbsum/7kep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kep ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Avibactam is a potent diazobicyclooctane inhibitor of class A and C beta-lactamases. The inhibitor also exhibits variable activity against some class D enzymes from Gram-negative bacteria; however, its interaction with recently discovered class D beta-lactamases from Gram-positive bacteria has not been studied. Here, we describe microbiological, kinetic, and mass spectrometry studies of the interaction of avibactam with CDD-1, a class D beta-lactamase from the clinically important pathogen Clostridioides difficile, and show that avibactam is a potent irreversible mechanism-based inhibitor of the enzyme. X-ray crystallographic studies at three time-points demonstrate the rapid formation of a stable CDD-1-avibactam acyl-enzyme complex and highlight differences in the anchoring of the inhibitor by class D enzymes from Gram-positive and Gram-negative bacteria.
		+
		+	Inhibition of the Clostridioides difficile Class D beta-Lactamase CDD-1 by Avibactam.,Stewart NK, Toth M, Stasyuk A, Lee M, Smith CA, Vakulenko SB ACS Infect Dis. 2021 Jan 3. doi: 10.1021/acsinfecdis.0c00714. PMID:33390002<ref>PMID:33390002</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kep" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus difficilis hall and o'toole 1935]]
		+	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Smith CA]]	+	[[Category: Smith, C A]]
-	[[Category: Stewart NK]]	+	[[Category: Stewart, N K]]
-	[[Category: Toth M]]	+	[[Category: Toth, M]]
-	[[Category: Vakulenko SB]]	+	[[Category: Vakulenko, S B]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Gram-positive]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-inhibitor complex]]
		+	[[Category: Inhibitor]]
		+	[[Category: Mutant]]

OCA at 08:14, 20 January 2021

OCA — Wed, 20 Jan 2021 08:14:46 GMT

←Older revision		Revision as of 08:14, 20 January 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7kep ~~is ON HOLD until Paper Publication~~	+	==avibactam-CDD-1 2 minute complex==
-		+	<StructureSection load='7kep' size='340' side='right'caption='[[7kep]]' scene=''>
-	~~Authors~~: ~~Smith~~, C.A., ~~Vakulenko~~, S.B., ~~Stewart, N~~.K., ~~Toth, M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KEP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7KEP FirstGlance]. <br>
-	~~Description: avibactam-CDD-1 2 minute complex~~	+	</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=7kep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kep OCA], [http://pdbe.org/7kep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7kep RCSB], [http://www.ebi.ac.uk/pdbsum/7kep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7kep ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Smith~~, C.A~~]]	+	__TOC__
-	[[Category: ~~Toth, M~~]]	+	</StructureSection>
-	[[Category: ~~Vakulenko, S.B~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Stewart, N.K~~]]	+	[[Category: Smith CA]]
		+	[[Category: Stewart NK]]
		+	[[Category: Toth M]]
		+	[[Category: Vakulenko SB]]

OCA: Protected "7kep" [edit=sysop:move=sysop]

OCA — Wed, 21 Oct 2020 06:53:15 GMT

Protected "7kep" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:53, 21 October 2020

OCA: New page: '''Unreleased structure''' The entry 7kep is ON HOLD until Paper Publication Authors: Smith, C.A., Vakulenko, S.B., Stewart, N.K., Toth, M. Description: avibactam-CDD-1 2 minute comple...

OCA — Wed, 21 Oct 2020 06:53:14 GMT

New page: '''Unreleased structure''' The entry 7kep is ON HOLD until Paper Publication Authors: Smith, C.A., Vakulenko, S.B., Stewart, N.K., Toth, M. Description: avibactam-CDD-1 2 minute comple...

New page

'''Unreleased structure'''

The entry 7kep is ON HOLD until Paper Publication

Authors: Smith, C.A., Vakulenko, S.B., Stewart, N.K., Toth, M.

Description: avibactam-CDD-1 2 minute complex
[[Category: Unreleased Structures]]
[[Category: Smith, C.A]]
[[Category: Toth, M]]
[[Category: Vakulenko, S.B]]
[[Category: Stewart, N.K]]

7kep - Revision history

OCA at 09:28, 26 May 2021

OCA at 08:14, 20 January 2021

OCA: Protected "7kep" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7kep is ON HOLD until Paper Publication Authors: Smith, C.A., Vakulenko, S.B., Stewart, N.K., Toth, M. Description: avibactam-CDD-1 2 minute comple...