3ZR9

Structure of New Delhi Metallo-Beta-lactamase 1 (NDM-1)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1).

Green, V.L., Verma, A., Owens, R.J., Phillips, S.E., Carr, S.B.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1160

  • DOI: https://doi.org/10.1107/S1744309111029654
  • Primary Citation of Related Structures:  
    3ZR9

  • PubMed Abstract: 

    Antibiotic resistance in bacterial pathogens poses a serious threat to human health and the metallo-β-lactamase (MBL) enzymes are responsible for much of this resistance. The recently identified New Delhi MBL 1 (NDM-1) is a novel member of this family that is capable of hydrolysing a wide variety of clinically important antibiotics. Here, the crystal structure of NDM-1 from Klebsiella pneumoniae is reported and its structure and active site are discussed in the context of other recently deposited coordinates of NDM-1.

    • Organizational Affiliation: 

    Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon OX11 0FA, England.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-LACTAMASE NDM-1231Klebsiella pneumoniaeMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae)
Explore C7C422 
Go to UniProtKB:  C7C422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7C422
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD
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E [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
ZN
Query on ZN
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B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO
Query on CO
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C [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
NI
Query on NI
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D [auth A],
F [auth A],
G [auth A],
H [auth A]		NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.3α = 90
b = 120.3β = 90
c = 88.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-08-03
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2011-11-30
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description