5zgz - Revision history

OCA at 08:54, 22 November 2023

OCA — Wed, 22 Nov 2023 08:54:41 GMT

←Older revision		Revision as of 08:54, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of NDM-1 at pH7.5 (Imidazole) with 1 molecule per asymmetric unit==		==Crystal structure of NDM-1 at pH7.5 (Imidazole) with 1 molecule per asymmetric unit==
-	<StructureSection load='5zgz' size='340' side='right' caption='[[5zgz]], [[Resolution\|resolution]] 0.95Å' scene=''>	+	<StructureSection load='5zgz' size='340' side='right'caption='[[5zgz]], [[Resolution\|resolution]] 0.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zgz]] 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=5ZGZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZGZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zgz]] 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=5ZGZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZGZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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]] 0.95Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xp6\|5xp6]]~~, [[~~5zgx~~\|~~5zgx]], [[5zgw\|5zgw]], [[5zgy\|5zgy~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>blaNDM-1 ([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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5zgz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zgz OCA], [https://pdbe.org/5zgz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zgz RCSB], [https://www.ebi.ac.uk/pdbsum/5zgz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zgz ProSAT]</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=5zgz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zgz OCA], [~~http~~://pdbe.org/5zgz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zgz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zgz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zgz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BLAN1_KLEPN BLAN1_KLEPN]] Confers resistance to many beta-lactam antibiotics, including some carbapenems. Does not confer resistance to the polymixin colistin or the fluoroquinolone ciprofloxacin.	+	[https://www.uniprot.org/uniprot/BLAN1_KLEPN BLAN1_KLEPN] Confers resistance to many beta-lactam antibiotics, including some carbapenems. Does not confer resistance to the polymixin colistin or the fluoroquinolone ciprofloxacin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5zgz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zgz" 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: ~~Hao, Q~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Zhang, H~~]]	+	[[Category: Hao Q]]
-	[[Category: ~~Antibiotic resistent]]~~	+	[[Category: Zhang H]]
-	~~[[Category: Conformational change]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metallo-beta-lactamase]]~~	+
-	~~[[Category: Ndm-1~~]]	+

OCA at 20:13, 19 September 2018

OCA — Wed, 19 Sep 2018 20:13:06 GMT

←Older revision		Revision as of 20:13, 19 September 2018
Line 3:		Line 3:
	<StructureSection load='5zgz' size='340' side='right' caption='[[5zgz]], [[Resolution\|resolution]] 0.95Å' scene=''>		<StructureSection load='5zgz' size='340' side='right' caption='[[5zgz]], [[Resolution\|resolution]] 0.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zgz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZGZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZGZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zgz]] 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=5ZGZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZGZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xp6\|5xp6]], [[5zgx\|5zgx]], [[5zgw\|5zgw]], [[5zgy\|5zgy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xp6\|5xp6]], [[5zgx\|5zgx]], [[5zgw\|5zgw]], [[5zgy\|5zgy]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaNDM-1 ([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='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=5zgz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zgz OCA], [http://pdbe.org/5zgz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zgz RCSB], [http://www.ebi.ac.uk/pdbsum/5zgz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zgz 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=5zgz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zgz OCA], [http://pdbe.org/5zgz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zgz RCSB], [http://www.ebi.ac.uk/pdbsum/5zgz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zgz ProSAT]</span></td></tr>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BLAN1_KLEPN BLAN1_KLEPN]] Confers resistance to many beta-lactam antibiotics, including some carbapenems. Does not confer resistance to the polymixin colistin or the fluoroquinolone ciprofloxacin.		[[http://www.uniprot.org/uniprot/BLAN1_KLEPN BLAN1_KLEPN]] Confers resistance to many beta-lactam antibiotics, including some carbapenems. Does not confer resistance to the polymixin colistin or the fluoroquinolone ciprofloxacin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Beta-lactam antibiotics are the mainstay for the treatment of bacterial infections. However, elevated resistance to these antibiotics mediated by metallo-beta-lactamases (MBL) has become a global concern. New Delhi metallo-beta-lactamase-1 (NDM-1), a newly added member of the MBL family that can hydrolyze almost all beta-lactam antibiotics, has rapidly spread all over the world and posed serious clinical threats. Broad-spectrum and mechanism-based inhibitors against all MBLs are highly desired, but the differential mechanisms of MBLs towards different antibiotics pose a great challenge. To facilitate the design of mechanism-based inhibitors, we investigated the active-site conformational changes of NDM-1 through the determination of a series of 15 high-resolution crystal structures in native form and in complex with products, biochemical and biophysical studies, site-directed mutagenesis and molecular dynamics computation. The structural studies reveal the consistency of the active site conformations in NDM-1/products complexes and the fluctuation in native NDM-1 structures. The enzymatic measurements indicate a correlation between enzymatic activity and the active site fluctuation with more fluctuation favoring higher activity. This correlation is further validated by structural and enzymatic studies of the Q123G mutant. Our combinational studies suggest that active site conformational fluctuation promotes the enzymatic activity of NDM-1, which may guide further mechanism studies and inhibitor design.
		+
		+	Active site conformational fluctuations promote the enzymatic activity of NDM-1.,Zhang H, Ma G, Zhu Y, Zeng L, Ahmad A, Wang C, Pang B, Fang H, Zhao L, Hao Q Antimicrob Agents Chemother. 2018 Aug 27. pii: AAC.01579-18. doi:, 10.1128/AAC.01579-18. PMID:30150473<ref>PMID:30150473</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zgz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:01, 22 August 2018

OCA — Wed, 22 Aug 2018 06:01:48 GMT

←Older revision		Revision as of 06:01, 22 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5zgz is ON HOLD until Paper Publication~~	+	==Crystal structure of NDM-1 at pH7.5 (Imidazole) with 1 molecule per asymmetric unit==
-		+	<StructureSection load='5zgz' size='340' side='right' caption='[[5zgz]], [[Resolution\|resolution]] 0.95Å' scene=''>
-	~~Authors: Zhang, H., Hao, Q.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zgz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZGZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZGZ FirstGlance]. <br>
-	~~Description:~~ Crystal structure of NDM-1 at pH7.5 (Imidazole) with 1 molecule per asymmetric unit	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xp6\|5xp6]], [[5zgx\|5zgx]], [[5zgw\|5zgw]], [[5zgy\|5zgy]]</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=5zgz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zgz OCA], [http://pdbe.org/5zgz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zgz RCSB], [http://www.ebi.ac.uk/pdbsum/5zgz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zgz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BLAN1_KLEPN BLAN1_KLEPN]] Confers resistance to many beta-lactam antibiotics, including some carbapenems. Does not confer resistance to the polymixin colistin or the fluoroquinolone ciprofloxacin.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
	[[Category: Hao, Q]]		[[Category: Hao, Q]]
	[[Category: Zhang, H]]		[[Category: Zhang, H]]
		+	[[Category: Antibiotic resistent]]
		+	[[Category: Conformational change]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallo-beta-lactamase]]
		+	[[Category: Ndm-1]]

OCA at 12:17, 11 April 2018

OCA — Wed, 11 Apr 2018 12:17:33 GMT

←Older revision		Revision as of 12:17, 11 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zgz is ON HOLD	+	The entry 5zgz is ON HOLD until Paper Publication

	Authors: Zhang, H., Hao, Q.		Authors: Zhang, H., Hao, Q.

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

OCA — Wed, 21 Mar 2018 05:58:53 GMT

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

←Older revision

Revision as of 05:58, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zgz is ON HOLD Authors: Zhang, H., Hao, Q. Description: Crystal structure of NDM-1 at pH7.5 (Imidazole) with 1 molecule per asymmetric unit [[Cate...

OCA — Wed, 21 Mar 2018 05:58:52 GMT

New page: '''Unreleased structure''' The entry 5zgz is ON HOLD Authors: Zhang, H., Hao, Q. Description: Crystal structure of NDM-1 at pH7.5 (Imidazole) with 1 molecule per asymmetric unit [[Cate...

New page

'''Unreleased structure'''

The entry 5zgz is ON HOLD

Authors: Zhang, H., Hao, Q.

Description: Crystal structure of NDM-1 at pH7.5 (Imidazole) with 1 molecule per asymmetric unit
[[Category: Unreleased Structures]]
[[Category: Hao, Q]]
[[Category: Zhang, H]]