6mkq - Revision history

OCA at 06:33, 11 October 2023

OCA — Wed, 11 Oct 2023 06:33:30 GMT

←Older revision		Revision as of 06:33, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6mkq' size='340' side='right'caption='[[6mkq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6mkq' size='340' side='right'caption='[[6mkq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mkq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mkq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MKQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=NXL:(2S~~,~~5R)-1-FORMYL-5-~~[~~(SULFOOXY)AMINO~~]~~PIPERIDINE-2-CARBOXAMIDE'>NXL</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]] 1.9Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</scene></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=6mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mkq OCA], [~~http~~://pdbe.org/6mkq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mkq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mkq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mkq 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=6mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mkq OCA], [https://pdbe.org/6mkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mkq RCSB], [https://www.ebi.ac.uk/pdbsum/6mkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mkq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0U3IB62_VIBCL A0A0U3IB62_VIBCL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillo virgola del koch trevisan 1884]]
-	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mark, B L]]
-	[[Category: Vadlamani, G]]
-	[[Category: Avibactam]]
-	[[Category: Carbapenemase]]
-	[[Category: Hydrolase]]
-	[[Category: Hydrolase-hydrolase inhibitor complex]]
-	[[Category: Vcc-1]]
	[[Category: Vibrio cholerae]]		[[Category: Vibrio cholerae]]
		+	[[Category: Mark BL]]
		+	[[Category: Vadlamani G]]

OCA at 09:05, 8 January 2020

OCA — Wed, 08 Jan 2020 09:05:47 GMT

←Older revision		Revision as of 09:05, 8 January 2020
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 6mkq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6mkq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:57, 10 April 2019

OCA — Wed, 10 Apr 2019 07:57:35 GMT

←Older revision		Revision as of 07:57, 10 April 2019
Line 1:		Line 1:

	==Carbapenemase VCC-1 bound to avibactam==		==Carbapenemase VCC-1 bound to avibactam==
-	<StructureSection load='6mkq' size='340' side='right' caption='[[6mkq]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6mkq' size='340' side='right'caption='[[6mkq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6mkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MKQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6mkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MKQ FirstGlance]. <br>
Line 23:		Line 23:
	[[Category: Bacillo virgola del koch trevisan 1884]]		[[Category: Bacillo virgola del koch trevisan 1884]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Mark, B L]]		[[Category: Mark, B L]]
	[[Category: Vadlamani, G]]		[[Category: Vadlamani, G]]

OCA at 08:30, 6 March 2019

OCA — Wed, 06 Mar 2019 08:30:43 GMT

←Older revision		Revision as of 08:30, 6 March 2019
Line 1:		Line 1:

	==Carbapenemase VCC-1 bound to avibactam==		==Carbapenemase VCC-1 bound to avibactam==
-	<StructureSection load='6mkq' size='340' side='right' caption='[[6mkq]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='6mkq' size='340' side='right' caption='[[6mkq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mkq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mkq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MKQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</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='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=6mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mkq OCA], [http://pdbe.org/6mkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mkq RCSB], [http://www.ebi.ac.uk/pdbsum/6mkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mkq 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=6mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mkq OCA], [http://pdbe.org/6mkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mkq RCSB], [http://www.ebi.ac.uk/pdbsum/6mkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mkq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In 2016 we identified a new class A carbapenemase, VCC-1, in nontoxigenic Vibrio cholerae that had been isolated from retail shrimp imported into Canada for human consumption. Shortly thereafter, seven additional VCC-1 producing V. cholerae were isolated along the German coastline. These isolates appear to have acquired the VCC-1 gene (bla VCC-1) independently from the Canadian isolate, suggesting bla VCC-1 is mobile and widely distributed. VCC-1 hydrolyzes penicillins, cephalothin, aztreonam, and carbapenems, and like the broadly disseminated class A carbapenemase KPC-2, is only weakly inhibited by clavulanic acid or tazobactam. Although VCC-1 has yet to observed in the clinic, its encroachment into aquaculture and other areas with human activity suggests the enzyme may be emerging as a public health threat. To pre-emptively address this threat, we examined the structural and functional biology of VCC-1 against the FDA approved non-beta-lactam-based inhibitor avibactam. We found that avibactam restored the in vitro sensitivity of V. cholerae to meropenem, impenem and ertapenem. Acylation efficiency was lower for VCC-1 as compared to KPC-2 and akin to that of Pseudomonas aeruginosa PAO1 AmpC (k2/Ki=3.0 x 10(3) M(-1)sec(-137)). The tertiary structure of VCC-1 is similar to that of KPC-2 and they bind avibactam similarly; however, our analyses suggest that VCC-1 may be unable to degrade avibactam as has been found for KPC-2. Based on our prior genomics-based surveillance, we were able to target VCC-1 for detailed molecular studies to gain early insights that could be used to combat this carbapenemse in the future.
		+
		+	Molecular basis for the potent inhibition of the emerging carbapenemase VCC-1 by avibactam.,Mangat CS, Vadlamani G, Holicek V, Chu M, Larmour V, Vocadlo DJ, Mulvey MR, Mark BL Antimicrob Agents Chemother. 2019 Feb 19. pii: AAC.02112-18. doi:, 10.1128/AAC.02112-18. PMID:30782990<ref>PMID:30782990</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6mkq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillo virgola del koch trevisan 1884]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Mark, B L]]		[[Category: Mark, B L]]

OCA at 08:43, 30 January 2019

OCA — Wed, 30 Jan 2019 08:43:10 GMT

←Older revision		Revision as of 08:43, 30 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6mkq is ~~ON HOLD until Paper Publication~~	+	==Carbapenemase VCC-1 bound to avibactam==
-		+	<StructureSection load='6mkq' size='340' side='right' caption='[[6mkq]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~: ~~Mark~~, B.L., ~~Vadlamani~~, G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6mkq]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MKQ FirstGlance]. <br>
-	~~Description~~: ~~Carbapenemase VCC~~-~~1 bound to avibactam~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NXL:(2S,5R)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>NXL</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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>
-	[[Category: Mark, B.L]]	+	<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=6mkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mkq OCA], [http://pdbe.org/6mkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mkq RCSB], [http://www.ebi.ac.uk/pdbsum/6mkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mkq ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Mark, B L]]
	[[Category: Vadlamani, G]]		[[Category: Vadlamani, G]]
		+	[[Category: Avibactam]]
		+	[[Category: Carbapenemase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Vcc-1]]
		+	[[Category: Vibrio cholerae]]

OCA at 06:29, 10 October 2018

OCA — Wed, 10 Oct 2018 06:29:32 GMT

←Older revision		Revision as of 06:29, 10 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6mkq is ON HOLD	+	The entry 6mkq is ON HOLD until Paper Publication

	Authors: Mark, B.L., Vadlamani, G.		Authors: Mark, B.L., Vadlamani, G.

OCA: Protected "6mkq" [edit=sysop:move=sysop]

OCA — Wed, 03 Oct 2018 06:29:48 GMT

Protected "6mkq" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:29, 3 October 2018

OCA: New page: '''Unreleased structure''' The entry 6mkq is ON HOLD Authors: Mark, B.L., Vadlamani, G. Description: Carbapenemase VCC-1 bound to avibactam Category: Unreleased Structures [[Catego...

OCA — Wed, 03 Oct 2018 06:29:47 GMT

New page: '''Unreleased structure''' The entry 6mkq is ON HOLD Authors: Mark, B.L., Vadlamani, G. Description: Carbapenemase VCC-1 bound to avibactam Category: Unreleased Structures [[Catego...

New page

'''Unreleased structure'''

The entry 6mkq is ON HOLD

Authors: Mark, B.L., Vadlamani, G.

Description: Carbapenemase VCC-1 bound to avibactam
[[Category: Unreleased Structures]]
[[Category: Mark, B.L]]
[[Category: Vadlamani, G]]