› 5y6e

X-ray diffraction
1.8Å resolution

VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 12)

Released:
DOI: 10.2210/pdb5y6e/pdb
PDB entry 5y6e coloured by chain, front view.
PDB entry 5y6e coloured by chain, side view.
PDB entry 5y6e coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
((S)-3-Mercapto-2-methylpropanamido)acetic acid derivatives as metallo-β-lactamase inhibitors: Synthesis, kinetic and crystallographic studies.
Liu S, Jing L, Yu ZJ, Wu C, Zheng Y, Zhang E, Chen Q, Yu Y, Guo L, Wu Y, Li GB
Eur J Med Chem 145 649-660 (2018)
PMID: 29353720

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-191748 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase type 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 231 amino acids
Theoretical weight: 24.68 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9K2N0 (Residues: 32-262; Coverage: 94%)
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 ZN 6 x ZN
Ligand 8PO 2 x 8PO
Ligand FMT 4 x FMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 101.355Å b: 74.452Å c: 64.456Å
α: 90° β: 129.46° γ: 90°
R-values:
R R work R free
0.138 0.136 0.173
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Targeting Metalloenzymes for Therapeutic Intervention.
Chen et al. (2019)
2 more

1 mention without citation

Discovery of [1,2,4]Triazole Derivatives as New Metallo-β-Lactamase Inhibitors.
Yuan et al. (2019)