6v7i - Revision history

OCA at 08:05, 11 October 2023

2023-10-11T08:05:17Z

←Older revision		Revision as of 08:05, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6v7i' size='340' side='right'caption='[[6v7i]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='6v7i' size='340' side='right'caption='[[6v7i]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6v7i]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus~~ pneumoniae~~" (schroeter 1886) flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V7I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6V7I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v7i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V7I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4D6:{(3R,6S)-2-HYDROXY-3-[(THIOPHEN-2-YLACETYL)AMINO]-1,2-OXABORINAN-6-YL}ACETIC+ACID'>4D6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.25Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla, kpc, kpc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4D6:{(3R,6S)-2-HYDROXY-3-[(THIOPHEN-2-YLACETYL)AMINO]-1,2-OXABORINAN-6-YL}ACETIC+ACID'>4D6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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'>[https://proteopedia.org/fgij/fg.htm?mol=6v7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v7i OCA], [https://pdbe.org/6v7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v7i RCSB], [https://www.ebi.ac.uk/pdbsum/6v7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v7i 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=6v7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v7i OCA], [~~http~~://pdbe.org/6v7i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6v7i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6v7i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6v7i ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BLKPC_KLEPN BLKPC_KLEPN]] Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency.	+	[https://www.uniprot.org/uniprot/BLKPC_KLEPN BLKPC_KLEPN] Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6v7i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6v7i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta-lactamase~~]]	+	[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, Y]]	+	[[Category: Chen Y]]
-	[[Category: Pemberton~~, O A]]~~	+	[[Category: Pemberton OA]]
-	~~[[Category: Boronate]]~~	+
-	~~[[Category: Carbapenemase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibitor~~]]	+

OCA at 11:33, 26 August 2020

2020-08-26T11:33:57Z

←Older revision		Revision as of 11:33, 26 August 2020
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BLKPC_KLEPN BLKPC_KLEPN]] Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency.		[[http://www.uniprot.org/uniprot/BLKPC_KLEPN BLKPC_KLEPN]] Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Class A beta-lactamases are a major cause of beta-lactam resistance in Gram-negative bacteria. The recent FDA approved cyclic boronate, vaborbactam, is a reversible covalent inhibitor of class A beta-lactamases including CTX-M extended-spectrum beta-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity towards these two enzymes, despite their similarity. A 1.0 A crystal structure of CTX-M-14 demonstrates that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25 A crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, and alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the beta3 strand on the inactivation rate, and the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved beta-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.
		+
		+	Structural basis and binding kinetics of vaborbactam in class A beta-lactamase inhibition.,Pemberton OA, Tsivkovski R, Totrov M, Lomovskaya O, Chen Y Antimicrob Agents Chemother. 2020 Aug 10. pii: AAC.00398-20. doi:, 10.1128/AAC.00398-20. PMID:32778546<ref>PMID:32778546</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6v7i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:35, 19 August 2020

2020-08-19T06:35:27Z

←Older revision		Revision as of 06:35, 19 August 2020
Line 1:		Line 1:

	==Structure of KPC-2 bound to Vaborbactam at 1.25 A==		==Structure of KPC-2 bound to Vaborbactam at 1.25 A==
-	<StructureSection load='6v7i' size='340' side='right'caption='[[6v7i]]' scene=''>	+	<StructureSection load='6v7i' size='340' side='right'caption='[[6v7i]], [[Resolution\|resolution]] 1.25Å' 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=6V7I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V7I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v7i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V7I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V7I 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=6v7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v7i OCA], [http://pdbe.org/6v7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v7i RCSB], [http://www.ebi.ac.uk/pdbsum/6v7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v7i 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=4D6:{(3R,6S)-2-HYDROXY-3-[(THIOPHEN-2-YLACETYL)AMINO]-1,2-OXABORINAN-6-YL}ACETIC+ACID'>4D6</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla, kpc, kpc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</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=6v7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v7i OCA], [http://pdbe.org/6v7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v7i RCSB], [http://www.ebi.ac.uk/pdbsum/6v7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v7i ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BLKPC_KLEPN BLKPC_KLEPN]] Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency.
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen Y]]	+	[[Category: Chen, Y]]
-	[[Category: Pemberton OA]]	+	[[Category: Pemberton, O A]]
		+	[[Category: Boronate]]
		+	[[Category: Carbapenemase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibitor]]

OCA at 09:47, 12 August 2020

2020-08-12T09:47:06Z

←Older revision		Revision as of 09:47, 12 August 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6v7i ~~is ON HOLD until Paper Publication~~	+	==Structure of KPC-2 bound to Vaborbactam at 1.25 A==
-		+	<StructureSection load='6v7i' size='340' side='right'caption='[[6v7i]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V7I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V7I FirstGlance]. <br>
-	~~Description~~:	+	</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=6v7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v7i OCA], [http://pdbe.org/6v7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v7i RCSB], [http://www.ebi.ac.uk/pdbsum/6v7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v7i ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen Y]]
		+	[[Category: Pemberton OA]]

OCA at 13:30, 29 January 2020

2020-01-29T13:30:52Z

←Older revision		Revision as of 13:30, 29 January 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6v7i is ON HOLD	+	The entry 6v7i is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6v7i" [edit=sysop:move=sysop]

2019-12-18T06:04:03Z

Protected "6v7i" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:04, 18 December 2019

OCA: New page: '''Unreleased structure''' The entry 6v7i is ON HOLD Authors: Description: Category: Unreleased Structures

2019-12-18T06:04:01Z

New page: '''Unreleased structure''' The entry 6v7i is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6v7i is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]