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

X-ray diffraction
1.91Å resolution
PDB entry 3zr9 coloured by chain, front view.
PDB entry 3zr9 coloured by chain, side view.
PDB entry 3zr9 coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Assemblies composition:
monomeric (preferred)
homo octamer
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Metallo-beta-lactamase type 2
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Multimeric state: monomeric
Accessible surface area: 9779.4 Å2
Buried surface area: 699.18 Å2
Dissociation area: 37.14 Å2
Dissociation energy (ΔGdiss): 3.54 kcal/mol
Dissociation entropy (TΔSdiss): -0.13 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111680
Assembly 2
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Assembly Name: Metallo-beta-lactamase type 2
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Multimeric state: homo octamer
Accessible surface area: 70979.28 Å2
Buried surface area: 12400.25 Å2
Dissociation area: 3,685.71 Å2
Dissociation energy (ΔGdiss): 11.33 kcal/mol
Dissociation entropy (TΔSdiss): 92.88 kcal/mol
Symmetry number: 8
PDBe Complex ID: PDB-CPX-111683

Macromolecules

Metallo-beta-lactamase type 2
Chain: A
Length: 231 amino acids
Theoretical weight: 24.34 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: C7C422 (Residues: 42-270; Coverage: 95%)
Gene name: blaNDM-1
Pfam: Metallo-beta-lactamase superfamily
InterPro:
CATH: Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Metallo-beta-lactamase type 2 in PDB entry 3zr9, assembly 1, front view.
Metallo-beta-lactamase type 2 in PDB entry 3zr9, assembly 1, side view.
Metallo-beta-lactamase type 2 in PDB entry 3zr9, assembly 1, top view.
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