4x68 - Revision history

OCA at 15:25, 8 November 2023

OCA — Wed, 08 Nov 2023 15:25:00 GMT

←Older revision		Revision as of 15:25, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x68]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X68 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X68 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x68]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X68 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X68 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</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]] 1.68Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene></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=4x68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x68 OCA], [https://pdbe.org/4x68 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x68 RCSB], [https://www.ebi.ac.uk/pdbsum/4x68 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x68 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=4x68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x68 OCA], [https://pdbe.org/4x68 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x68 RCSB], [https://www.ebi.ac.uk/pdbsum/4x68 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x68 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:15, 12 April 2023

OCA — Wed, 12 Apr 2023 21:15:11 GMT

←Older revision		Revision as of 21:15, 12 April 2023
Line 3:		Line 3:
	<StructureSection load='4x68' size='340' side='right'caption='[[4x68]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='4x68' size='340' side='right'caption='[[4x68]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x68]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X68 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X68 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x68]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X68 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X68 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x69\|4x69]]</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=4x68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x68 OCA], [https://pdbe.org/4x68 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x68 RCSB], [https://www.ebi.ac.uk/pdbsum/4x68 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x68 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, PA4110 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=4x68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x68 OCA], [~~http~~://pdbe.org/4x68 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x68 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x68 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x68 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AMPC_PSEAE AMPC_PSEAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Watanabe, T]]	+	[[Category: Watanabe T]]
-	[[Category: Yamada, M]]	+	[[Category: Yamada M]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 07:08, 29 May 2019

OCA — Wed, 29 May 2019 07:08:00 GMT

←Older revision		Revision as of 07:08, 29 May 2019
Line 1:		Line 1:
		+
	==Crystal Structure of OP0595 complexed with AmpC==		==Crystal Structure of OP0595 complexed with AmpC==
-	<StructureSection load='4x68' size='340' side='right' caption='[[4x68]], [[Resolution\|resolution]] 1.68Å' scene=''>	+	<StructureSection load='4x68' size='340' side='right'caption='[[4x68]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x68]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X68 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X68 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x68]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X68 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X68 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x69\|4x69]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x69\|4x69]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, PA4110 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=4x68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x68 OCA], [http://pdbe.org/4x68 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x68 RCSB], [http://www.ebi.ac.uk/pdbsum/4x68 PDBsum]</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=4x68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x68 OCA], [http://pdbe.org/4x68 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x68 RCSB], [http://www.ebi.ac.uk/pdbsum/4x68 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x68 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4x68" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4x68" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
		+	[[Category: Pseae]]
	[[Category: Watanabe, T]]		[[Category: Watanabe, T]]
	[[Category: Yamada, M]]		[[Category: Yamada, M]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 21:42, 15 October 2015

OCA — Thu, 15 Oct 2015 21:42:57 GMT

←Older revision		Revision as of 21:42, 15 October 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x69\|4x69]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x69\|4x69]]</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=4x68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x68 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x68 RCSB], [http://www.ebi.ac.uk/pdbsum/4x68 PDBsum]</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=4x68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x68 OCA], [http://pdbe.org/4x68 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x68 RCSB], [http://www.ebi.ac.uk/pdbsum/4x68 PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4x68" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:06, 1 July 2015

OCA — Wed, 01 Jul 2015 12:06:54 GMT

←Older revision		Revision as of 12:06, 1 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal Structure of OP0595 complexed with AmpC==
		+	<StructureSection load='4x68' size='340' side='right' caption='[[4x68]], [[Resolution\|resolution]] 1.68Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4x68]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X68 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X68 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OP0:(2S,5R)-N-(2-AMINOETHOXY)-1-FORMYL-5-[(SULFOOXY)AMINO]PIPERIDINE-2-CARBOXAMIDE'>OP0</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x69\|4x69]]</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=4x68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x68 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x68 RCSB], [http://www.ebi.ac.uk/pdbsum/4x68 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	OBJECTIVES: The production of a growing diversity of beta-lactamases by Gram-negative bacteria challenges antimicrobial chemotherapy. OP0595, discovered separately by each of Meiji Seika Pharma and Fedora Pharmaceuticals, is a new diazabicyclooctane serine beta-lactamase inhibitor that also acts as an antibiotic and as a beta-lactamase-independent beta-lactam 'enhancer'. METHODS: Inhibitory activity against serine beta-lactamases and affinity for PBPs were determined using nitrocefin and Bocillin FL, respectively. MICs alone and in combination with beta-lactam agents were measured according to CLSI recommendations. Morphological changes in Escherichia coli were examined by phase-contrast microscopy. RESULTS: IC50s of OP0595 for class A and C beta-lactamases were <1000 nM, with covalent binding demonstrated to the active-site serine of CTX-M-44 and AmpC enzymes. OP0595 also had direct antibiotic activity against many Enterobacteriaceae, associated with inhibition of PBP2 and conversion of the bacteria into spherical forms. Synergy between OP0595 and beta-lactam agents was seen against strains producing class A and C beta-lactamases vulnerable to inhibition. Lastly, OP0595 lowered the MICs of PBP3-targeted partner beta-lactam agents for a non-beta-lactamase-producing E. coli mutant that was resistant to OP0595 itself, indicating beta-lactamase-independent 'enhancer'-based synergy. CONCLUSIONS: OP0595 acts in three ways: (i) as an inhibitor of class A and C beta-lactamases, covalently binding at their active sites; (ii) as an antibacterial, by inhibiting PBP2 of several Enterobacteriaceae; and (iii) as an 'enhancer' of beta-lactam agents that bind to other PBPs besides PBP2 for several Enterobacteriaceae. OP0595 has considerable potential to overcome resistance when it is combined with various beta-lactam agents.

-	~~The entry 4x68 is ON HOLD until Paper Publication~~	+	OP0595, a new diazabicyclooctane: mode of action as a serine beta-lactamase inhibitor, antibiotic and beta-lactam 'enhancer'.,Morinaka A, Tsutsumi Y, Yamada M, Suzuki K, Watanabe T, Abe T, Furuuchi T, Inamura S, Sakamaki Y, Mitsuhashi N, Ida T, Livermore DM J Antimicrob Chemother. 2015 Jun 18. pii: dkv166. PMID:26089439<ref>PMID:26089439</ref>

-	~~Authors: Yamada~~, M.~~, Watanabe, T~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Watanabe, T]]
	[[Category: Yamada, M]]		[[Category: Yamada, M]]
-	[[Category: ~~Watanabe, T~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 20:32, 24 December 2014

OCA — Wed, 24 Dec 2014 20:32:58 GMT

←Older revision		Revision as of 20:32, 24 December 2014
Line 5:		Line 5:
	Authors: Yamada, M., Watanabe, T.		Authors: Yamada, M., Watanabe, T.

-	Description:	+	Description:
		+	[[Category: Unreleased Structures]]
		+	[[Category: Yamada, M]]
		+	[[Category: Watanabe, T]]

OCA: Protected "4x68" [edit=sysop:move=sysop]

OCA — Wed, 17 Dec 2014 11:43:24 GMT

Protected "4x68" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:43, 17 December 2014

OCA: New page: '''Unreleased structure''' The entry 4x68 is ON HOLD until Paper Publication Authors: Yamada, M., Watanabe, T. Description:

OCA — Wed, 17 Dec 2014 11:43:23 GMT

New page: '''Unreleased structure''' The entry 4x68 is ON HOLD until Paper Publication Authors: Yamada, M., Watanabe, T. Description:

New page

'''Unreleased structure'''

The entry 4x68 is ON HOLD until Paper Publication

Authors: Yamada, M., Watanabe, T.

Description: