5y5b - Revision history

OCA at 08:22, 22 November 2023

OCA — Wed, 22 Nov 2023 08:22:03 GMT

←Older revision		Revision as of 08:22, 22 November 2023
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	<StructureSection load='5y5b' size='340' side='right'caption='[[5y5b]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5y5b' size='340' side='right'caption='[[5y5b]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y5b]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus~~ marcescens~~" (bizio 1823) trevisan in de toni and trevisan 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y5B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y5b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y5B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.7Å</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5y5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y5b OCA], [~~http~~://pdbe.org/5y5b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y5b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y5b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y5b 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=5y5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y5b OCA], [https://pdbe.org/5y5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y5b RCSB], [https://www.ebi.ac.uk/pdbsum/5y5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y5b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BLAB_SERMA BLAB_SERMA]] Confers resistance to imipenem and broad-spectrum beta-lactams. Also hydrolyzes carbapenems.	+	[https://www.uniprot.org/uniprot/BLAB_SERMA BLAB_SERMA] Confers resistance to imipenem and broad-spectrum beta-lactams. Also hydrolyzes carbapenems.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Wachino, J~~]]	+	[[Category: Serratia marcescens]]
-	[[Category: ~~Hydrolase~~]]	+	[[Category: Wachino J]]

OCA at 07:20, 19 February 2020

OCA — Wed, 19 Feb 2020 07:20:40 GMT

←Older revision		Revision as of 07:20, 19 February 2020
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	==Crystal Structure Of IMP-1 Metallo-beta-lactamase==		==Crystal Structure Of IMP-1 Metallo-beta-lactamase==
-	<StructureSection load='5y5b' size='340' side='right' caption='[[5y5b]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5y5b' size='340' side='right'caption='[[5y5b]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y5b]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y5B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y5b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus marcescens" (bizio 1823) trevisan in de toni and trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y5B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BLAB_SERMA BLAB_SERMA]] Confers resistance to imipenem and broad-spectrum beta-lactams. Also hydrolyzes carbapenems.		[[http://www.uniprot.org/uniprot/BLAB_SERMA BLAB_SERMA]] Confers resistance to imipenem and broad-spectrum beta-lactams. Also hydrolyzes carbapenems.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The number of cases of infection with carbapenem-resistant Enterobacteriaceae (CRE) has been increasing and has become a major clinical and public health concern. Production of metallo-beta-lactamases (MBLs) is one of the principal carbapenem resistance mechanisms in CRE. Therefore, developing MBL inhibitors is a promising strategy to overcome the problems of carbapenem resistance conferred by MBLs. To date, the development and evaluation of MBL inhibitors have focused on subclass B1 MBLs but not on B3 MBLs. In the present study, we searched for B3 MBL (specifically, SMB-1) inhibitors and found thiosalicylic acid (TSA) to be a potent inhibitor of B3 SMB-1 MBL (50% inhibitory concentration [IC50], 0.95 muM). TSA inhibited the purified SMB-1 to a considerable degree but was not active against Escherichia coli cells producing SMB-1, as the meropenem (MEM) MIC for the SMB-1 producer was only slightly reduced with TSA. We then introduced a primary amine to TSA and synthesized 4-amino-2-sulfanylbenzoic acid (ASB), which substantially reduced the MEM MICs for SMB-1 producers. X-ray crystallographic analyses revealed that ASB binds to the two zinc ions, Ser221, and Thr223 at the active site of SMB-1. These are ubiquitously conserved residues across clinically relevant B3 MBLs. ASB also significantly inhibited other B3 MBLs, including AIM-1, LMB-1, and L1. Therefore, the characterization of ASB provides a starting point for the development of optimum B3 MBL inhibitors.
		+
		+	4-Amino-2-Sulfanylbenzoic Acid as a Potent Subclass B3 Metallo-beta-Lactamase-Specific Inhibitor Applicable for Distinguishing Metallo-beta-Lactamase Subclasses.,Wachino JI, Kanechi R, Nishino E, Mochizuki M, Jin W, Kimura K, Kurosaki H, Arakawa Y Antimicrob Agents Chemother. 2019 Sep 23;63(10). pii: AAC.01197-19. doi:, 10.1128/AAC.01197-19. Print 2019 Oct. PMID:31405855<ref>PMID:31405855</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y5b" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Wachino, J]]		[[Category: Wachino, J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 21:42, 9 August 2018

OCA — Thu, 09 Aug 2018 21:42:51 GMT

←Older revision		Revision as of 21:42, 9 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y5b is ~~ON HOLD until Aug 08 2019~~	+	==Crystal Structure Of IMP-1 Metallo-beta-lactamase==
-		+	<StructureSection load='5y5b' size='340' side='right' caption='[[5y5b]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors~~: ~~Wachino~~, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y5b]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y5B FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure Of IMP~~-~~1 Metallo~~-beta-~~lactamase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>
		+	<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=5y5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y5b OCA], [http://pdbe.org/5y5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y5b RCSB], [http://www.ebi.ac.uk/pdbsum/5y5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y5b ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BLAB_SERMA BLAB_SERMA]] Confers resistance to imipenem and broad-spectrum beta-lactams. Also hydrolyzes carbapenems.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
	[[Category: Wachino, J]]		[[Category: Wachino, J]]
		+	[[Category: Hydrolase]]

OCA: Protected "5y5b" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:09:17 GMT

Protected "5y5b" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:09, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y5b is ON HOLD until Aug 08 2019 Authors: Wachino, J. Description: Crystal Structure Of IMP-1 Metallo-beta-lactamase [[Category: Unreleased Struct...

OCA — Wed, 27 Sep 2017 16:09:15 GMT

New page: '''Unreleased structure''' The entry 5y5b is ON HOLD until Aug 08 2019 Authors: Wachino, J. Description: Crystal Structure Of IMP-1 Metallo-beta-lactamase [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 5y5b is ON HOLD until Aug 08 2019

Authors: Wachino, J.

Description: Crystal Structure Of IMP-1 Metallo-beta-lactamase
[[Category: Unreleased Structures]]
[[Category: Wachino, J]]