› 6ogo

X-ray diffraction
1.43Å resolution

Crystal structure of NDM-9 metallo-beta-lactamase

Released:
DOI: 10.2210/pdb6ogo/pdb
PDB entry 6ogo coloured by chain, front view.
PDB entry 6ogo coloured by chain, side view.
PDB entry 6ogo coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Flexible loops of New Delhi metallo-β-lactamase modulate its activity towards different substrates.
Raczynska JE, Imiolczyk B, Komorowska M, Sliwiak J, Czyrko-Horczak J, Brzezinski K, Jaskolski M
Int J Biol Macromol 158 104-115 (2020)
PMID: 32353499

Function and Biology Details

Reaction catalysed: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-495886 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase type 2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 243 amino acids
Theoretical weight: 25.69 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1M2CSI6 (Residues: 29-270; Coverage: 90%)
Gene names: BK300_27775, BK383_27845
Sequence domains: Metallo-beta-lactamase superfamily

Ligands and Environments

7 bound ligands:
Ligand ZN 6 x ZN
Ligand CL 9 x CL
Ligand PO4 3 x PO4
Ligand EDO 4 x EDO
Ligand PEG 4 x PEG
Ligand PGE 2 x PGE
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P31
Unit cell:
a: 122.929Å b: 122.929Å c: 38.501Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.075 0.074 0.116
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design.
Bahr et al. (2021)
1 more

1 mention without citation

In silico vaccine design and epitope mapping of New Delhi metallo-beta-lactamase (NDM): an immunoinformatics approach.
Fathollahi et al. (2021)