› 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 5o7n coloured by chain and viewed from the front.
PDB 5o7n coloured by chain and viewed from the side.
PDB 5o7n coloured by chain and viewed from the top.
Source organism: Klebsiella pneumoniae
Primary publication:
Challenges in the Development of a Thiol-Based Broad-Spectrum Inhibitor for Metallo-��-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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase domain-containing protein 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)

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Citations

7 review citations

Drug repurposing for next-generation combination therapies against multidrug-resistant bacteria.
Liu et al. (2021)
6 more