› 5k48

X-ray diffraction
1.74Å resolution

VIM-2 Metallo Beta Lactamase in complex with 3-(mercaptomethyl)-[1,1'-biphenyl]-4-carboxylic acid

Released:
DOI: 10.2210/pdb5k48/pdb
PDB entry 5k48 coloured by chain, front view.
PDB entry 5k48 coloured by chain, side view.
PDB entry 5k48 coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-β-lactamase Inhibitors.
Cain R, Brem J, Zollman D, McDonough MA, Johnson RM, Spencer J, Makena A, Abboud MI, Cahill S, Lee SY, McHugh PJ, Schofield CJ, Fishwick CWG
J Med Chem 61 1255-1260 (2018)
PMID: 29271657

Function and Biology Details

Reaction catalysed: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191748 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase type 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 242 amino acids
Theoretical weight: 25.69 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9K2N0 (Residues: 27-266; Coverage: 98%)
Gene names: PAERUG_P19_London_7_VIM_2_05_10_01672, bla vim-2, blaVIM-2, blm
Sequence domains: Metallo-beta-lactamase superfamily
Structure domains: Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Ligands and Environments

3 bound ligands:
Ligand S5Z 2 x S5Z
Ligand FMT 5 x FMT
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: C2
Unit cell:
a: 102.888Å b: 79.542Å c: 67.892Å
α: 90° β: 130.6° γ: 90°
R-values:
R R work R free
0.167 0.166 0.194
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Antibiotic resistance breakers: current approaches and future directions.
Laws et al. (2019)
9 more