6ttc: Difference between revisions
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==Haddock model of NDM-1/myricetin complex== | |||
<StructureSection load='6ttc' size='340' side='right'caption='[[6ttc]], [[NMR_Ensembles_of_Models | 4 NMR models]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6ttc]] 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=6TTC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TTC FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MYC:3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE'>MYC</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=6ttc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ttc OCA], [https://pdbe.org/6ttc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ttc RCSB], [https://www.ebi.ac.uk/pdbsum/6ttc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ttc ProSAT]</span></td></tr> | |||
</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> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6ttc" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Cintrat, J C]] | |||
[[Category: Crechet, J B]] | |||
[[Category: Gayral, M]] | |||
[[Category: Giraud, F]] | |||
[[Category: Guittet, E]] | |||
[[Category: Heijenoort, C van]] | |||
[[Category: Iorga, B I]] | |||
[[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: Antimicrobial resistance]] | |||
[[Category: Complex]] | |||
[[Category: Haddock]] | |||
[[Category: Inhibitor]] | |||
[[Category: Metal binding protein]] | |||
[[Category: Myricetin]] | |||
[[Category: New-delhi metallo-beta-lactamase-1]] | |||