› 5o7n

X-ray diffraction
1.5Å resolution

Beta-lactamase VIM-2 in complex with (2R)-1-(2-Benzyl-3-mercaptopropanoyl)piperidine-2-carboxylic acid

Released:
DOI: 10.2210/pdb5o7n/pdb
PDB entry 5o7n coloured by chain, front view.
PDB entry 5o7n coloured by chain, side view.
PDB entry 5o7n coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
Challenges in the Development of a Thiol-Based Broad-Spectrum Inhibitor for Metallo-β-Lactamases.
Büttner D, Kramer JS, Klingler FM, Wittmann SK, Hartmann MR, Kurz CG, Kohnhäuser D, Weizel L, Brüggerhoff A, Frank D, Steinhilber D, Wichelhaus TA, Pogoryelov D, Proschak E
ACS Infect Dis 4 360-372 (2018)
PMID: 29172434

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-103110 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase type 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 254 amino acids
Theoretical weight: 27.35 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A173FE28 (Residues: 9-248; Coverage: 97%)
Gene name: blaVIM-2
Sequence domains: Metallo-beta-lactamase superfamily

Ligands and Environments

4 bound ligands:
Ligand ZN 8 x ZN
Ligand 9NK 2 x 9NK
Ligand FMT 8 x FMT
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Spacegroup: C2
Unit cell:
a: 101.989Å b: 79.308Å c: 67.645Å
α: 90° β: 130.45° γ: 90°
R-values:
R R work R free
0.187 0.187 0.211
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Metallo-ß-lactamases: a review.
Behzadi et al. (2020)
9 more