6TT8 | pdb_00006tt8

Haddock model of NDM-1/morin complex

• PDB DOI: https://doi.org/10.2210/pdb6TT8/pdb
• BMRB: 34471

• Classification: METAL BINDING PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-25 Released: 2021-01-13 
• Deposition Author(s): Riviere, G., Oueslati, S., Gayral, M., Crechet, J.B., Nhiri, N., Jacquet, E., Cintrat, J.C., Giraud, F., van Heijenoort, C., Lescop, E., Pethe, S., Iorga, B.I., Naas, T., Guittet, E., Morellet, N.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 2800 
• Conformers Submitted: 56 
• Selection Criteria: target function 

Literature

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, J.B., Nhiri, N., Jacquet, E., Cintrat, J.C., Giraud, F., van Heijenoort, C., Lescop, E., Pethe, S., Iorga, B.I., Naas, T., Guittet, E., Morellet, N.

(2020) ACS Omega 5: 10466-10480

• PubMed: 32426604 
• DOI: https://doi.org/10.1021/acsomega.0c00590
• Primary Citation Related Structures: 
  6TT8, 6TTA, 6TTC


• PubMed Abstract: 
  

  New Delhi metallo-β-lactamase-1 (NDM-1) has recently emerged as a global threat because of its ability to confer resistance to all common β-lactam antibiotics. Understanding the molecular basis of β-lactam hydrolysis by NDM is crucial for designing NDM inhibitors or β-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 α2. 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.

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Organizational Affiliation: 
• Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France.
EA7361 "Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases", Faculty of Medicine, Université Paris-Sud, Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France.
Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris Sud, Université Paris-Saclay, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France.
Ecole Polytechnique, Route de Saclay, F-91120 Palaiseau, France.
Service de Chimie Bio-organique et Marquage (SCBM), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif/Yvette, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.41 kDa 
• Atom Count: 1,711 
• Modeled Residue Count: 227 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo beta lactamase NDM-1	A	227	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  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 EC: 3.5.2.6
UniProt
Find proteins for E9NWK5 (Klebsiella pneumoniae) Explore E9NWK5  Go to UniProtKB:  E9NWK5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRI (Subject of Investigation/LOI)	D [auth A]	2-[2,4-bis(oxidanyl)phenyl]-3,5,7-tris(oxidanyl)chromen-4-one C15 H10 O7 YXOLAZRVSSWPPT-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 2800 
• Conformers Submitted: 56 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Riviere, G., Oueslati, S., Gayral, M., Crechet, J.B., Nhiri, N., Jacquet, E., Cintrat, J.C., Giraud, F., van Heijenoort, C., Lescop, E., Pethe, S., Iorga, B.I., Naas, T., Guittet, E., Morellet, N.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-10-LABX-33

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-03-17
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references