Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pnueumoniae

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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This is version 1.5 of the entry. See complete history


Structure of Apo- and Monometalated Forms of NDM-1 A Highly Potent Carbapenem-Hydrolyzing Metallo-beta-Lactamase

Kim, Y.Tesar, C.Mire, J.Jedrzejczak, R.Binkowski, A.Babnigg, G.Sacchettini, J.Joachimiak, A.

(2011) PLoS One 6: e24621-e24621

  • DOI: https://doi.org/10.1371/journal.pone.0024621
  • Primary Citation of Related Structures:  
    3RKJ, 3RKK, 3SBL, 3SFP

  • PubMed Abstract: 

    The New Delhi Metallo-β-lactamase (NDM-1) gene makes multiple pathogenic microorganisms resistant to all known β-lactam antibiotics. The rapid emergence of NDM-1 has been linked to mobile plasmids that move between different strains resulting in world-wide dissemination. Biochemical studies revealed that NDM-1 is capable of efficiently hydrolyzing a wide range of β-lactams, including many carbapenems considered as "last resort" antibiotics. The crystal structures of metal-free apo- and monozinc forms of NDM-1 presented here revealed an enlarged and flexible active site of class B1 metallo-β-lactamase. This site is capable of accommodating many β-lactam substrates by having many of the catalytic residues on flexible loops, which explains the observed extended spectrum activity of this zinc dependent β-lactamase. Indeed, five loops contribute "keg" residues in the active site including side chains involved in metal binding. Loop 1 in particular, shows conformational flexibility, apparently related to the acceptance and positioning of substrates for cleavage by a zinc-activated water molecule.

  • Organizational Affiliation

    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase NDM-1
A, B
235Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.712α = 90
b = 51.113β = 106.96
c = 70.68γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-21
    Changes: Database references
  • Version 1.3: 2011-09-28
    Changes: Experimental preparation
  • Version 1.4: 2012-03-28
    Changes: Database references
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description