OCA at 06:52, 17 March 2021

OCA — Wed, 17 Mar 2021 06:52:36 GMT

←Older revision		Revision as of 06:52, 17 March 2021
Line 1:		Line 1:

	==Haddock model of NDM-1/quercetin complex==		==Haddock model of NDM-1/quercetin complex==
-	<StructureSection load='6tta' size='340' side='right'caption='[[6tta]]' scene=''>	+	<StructureSection load='6tta' size='340' side='right'caption='[[6tta]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' 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=6TTA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TTA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tta]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TTA 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=6tta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tta OCA], [~~http~~://pdbe.org/6tta PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tta RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tta PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tta 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=QUE:3,5,7,3,4-PENTAHYDROXYFLAVONE'>QUE</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, bla NDM-1, blaNDM-1_1, blaNDM-1_2, blaNDM-1_3, blaNDM1, NDM-1, BANRA_05884, C3483_29595, C7V41_28630, D647_p47098, EC13450_007, FAQ72_26810, FAQ97_27095, FAS39_27275, NCTC13443_00040, p2146_00143, pCRE380_21, PMK1_ndm00067, PMK1_ndm00076, PMK1_ndm00085, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3531848_05178, TR3_031, TR4_031 ([https://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=6tta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tta OCA], [https://pdbe.org/6tta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tta RCSB], [https://www.ebi.ac.uk/pdbsum/6tta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tta ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	New Delhi metallo-beta-lactamase-1 (NDM-1) has recently emerged as a global threat because of its ability to confer resistance to all common beta-lactam antibiotics. Understanding the molecular basis of beta-lactam hydrolysis by NDM is crucial for designing NDM inhibitors or beta-lactams resistant to their hydrolysis. In this study, for the first time, NMR was used to study the influence of Zn(II) ions on the dynamic behavior of NDM-1. Our results highlighted that the binding of Zn(II) in the NDM-1 active site induced several structural and dynamic changes on active site loop 2 (ASL2) and L9 loops and on helix alpha2. We subsequently studied the interaction of several flavonols: morin, quercetin, and myricetin were identified as natural and specific inhibitors of NDM-1. Quercetin conjugates were also synthesized in an attempt to increase the solubility and bioavailability. Our NMR investigations on NDM-1/flavonol interactions highlighted that both Zn(II) ions and the residues of the NDM-1 ASL1, ASL2, and ASL4 loops are involved in the binding of flavonols. This is the first NMR interaction study of NDM-1/inhibitors, and the models generated using HADDOCK will be useful for the rational design of more active inhibitors, directed against NDM-1.
		+
		+	NMR Characterization of the Influence of Zinc(II) Ions on the Structural and Dynamic Behavior of the New Delhi Metallo-beta-Lactamase-1 and on the Binding with Flavonols as Inhibitors.,Riviere G, Oueslati S, Gayral M, Crechet JB, Nhiri N, Jacquet E, Cintrat JC, Giraud F, van Heijenoort C, Lescop E, Pethe S, Iorga BI, Naas T, Guittet E, Morellet N ACS Omega. 2020 Apr 28;5(18):10466-10480. doi: 10.1021/acsomega.0c00590., eCollection 2020 May 12. PMID:32426604<ref>PMID:32426604</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tta" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cintrat JC]]	+	[[Category: Cintrat, J C]]
-	[[Category: Crechet JB]]	+	[[Category: Crechet, J B]]
-	[[Category: Gayral M]]	+	[[Category: Gayral, M]]
-	[[Category: Giraud F]]	+	[[Category: Giraud, F]]
-	[[Category: Guittet E]]	+	[[Category: Guittet, E]]
-	[[Category: Iorga BI]]	+	[[Category: Heijenoort, C van]]
-	[[Category: Jacquet E]]	+	[[Category: Iorga, B I]]
-	[[Category: Lescop E]]	+	[[Category: Jacquet, E]]
-	[[Category: Morellet N]]	+	[[Category: Lescop, E]]
-	[[Category: Naas T]]	+	[[Category: Morellet, N]]
-	[[Category: Nhiri N]]	+	[[Category: Naas, T]]
-	[[Category: Oueslati S]]	+	[[Category: Nhiri, N]]
-	[[Category: Pethe S]]	+	[[Category: Oueslati, S]]
-	[[Category: Riviere G]]	+	[[Category: Pethe, S]]
-	[[Category: ~~Van Heijenoort C~~]]	+	[[Category: Riviere, G]]
		+	[[Category: Antimicrobial resistance]]
		+	[[Category: Complex]]
		+	[[Category: Haddock]]
		+	[[Category: Inhibitor]]
		+	[[Category: Metal binding protein]]
		+	[[Category: New-delhi metallo-beta-lactamase-1]]
		+	[[Category: Quercetin]]

OCA at 05:48, 20 January 2021

OCA — Wed, 20 Jan 2021 05:48:16 GMT

←Older revision		Revision as of 05:48, 20 January 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6tta is ~~ON HOLD until Paper Publication~~	+	==Haddock model of NDM-1/quercetin complex==
-		+	<StructureSection load='6tta' size='340' side='right'caption='[[6tta]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TTA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TTA 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=6tta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tta OCA], [http://pdbe.org/6tta PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tta RCSB], [http://www.ebi.ac.uk/pdbsum/6tta PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tta ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cintrat JC]]
		+	[[Category: Crechet JB]]
		+	[[Category: Gayral M]]
		+	[[Category: Giraud F]]
		+	[[Category: Guittet E]]
		+	[[Category: Iorga BI]]
		+	[[Category: Jacquet E]]
		+	[[Category: Lescop E]]
		+	[[Category: Morellet N]]
		+	[[Category: Naas T]]
		+	[[Category: Nhiri N]]
		+	[[Category: Oueslati S]]
		+	[[Category: Pethe S]]
		+	[[Category: Riviere G]]
		+	[[Category: Van Heijenoort C]]

OCA at 06:23, 22 July 2020

OCA — Wed, 22 Jul 2020 06:23:05 GMT

←Older revision		Revision as of 06:23, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 08 Jan 2020 06:02:33 GMT

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

←Older revision

Revision as of 06:02, 8 January 2020

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

OCA — Wed, 08 Jan 2020 06:02:32 GMT

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

New page

'''Unreleased structure'''

The entry 6tta is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6tta - Revision history

OCA at 06:52, 17 March 2021

OCA at 05:48, 20 January 2021

OCA at 06:23, 22 July 2020

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

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