› 5ypl

X-ray diffraction
1.8Å resolution

Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EP complex

Released:
DOI: 10.2210/pdb5ypl/pdb
PDB entry 5ypl coloured by chain, front view.
PDB entry 5ypl coloured by chain, side view.
PDB entry 5ypl coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.
Feng H, Liu X, Wang S, Fleming J, Wang DC, Liu W
OpenAccess logo Nat Commun 8 2242 (2017)
PMID: 29269938

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-122980 (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: 25.63 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: E5KIY2 (Residues: 29-270; Coverage: 90%)
Gene names: AZ95_0035, BANRA_05542, E4K51_24975, ECS01_0033, G5603_25730, HIA71_26840, HIA71_28110, NDM1Dok01_N0175, P6223_005359, P6223_006060, RZR61_25285, bla NDM-1, blaNDM-1, pNDM102337_147, pNDM10505_149
Sequence domains: Metallo-beta-lactamase superfamily
Structure domains: Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand HIW 2 x HIW
Ligand SO4 1 x SO4
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 69.22Å b: 73.76Å c: 77.43Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.204
Expression system: Escherichia coli

Quick links

Citations

8 review citations

β-Lactamases and β-Lactamase Inhibitors in the 21st Century.
Tooke et al. (2019)
7 more

6 mentions without citation

The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.
Feng et al. (2017)
5 more