› 8gpd

X-ray diffraction
1.4Å resolution

Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin V

Released:
DOI: 10.2210/pdb8gpd/pdb
PDB entry 8gpd coloured by chain, front view.
PDB entry 8gpd coloured by chain, side view.
PDB entry 8gpd coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
Interplay between the β-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design.
Shi X, Dai Y, Lan Z, Wang S, Cui L, Xiao C, Zhao K, Li X, Liu W, Zhang Q
Int J Biol Macromol 262 130041 (2024)
PMID: 38336327

Function and Biology Details

Reaction catalysed: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123186 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase type 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 270 amino acids
Theoretical weight: 28.53 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E9NWK5 (Residues: 1-270; Coverage: 100%)
Gene names: APT92_09815, D647_p47098, EC13450_007, G4V31_29050, MYA94_26190, NCTC13443_00040, NDM-1, SAMEA3499901_05193, TR3_031, TR4_031, bla NDM-1, blaNDM-1, blaNDM1, p2146_00143, pCRE380_21, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138
Sequence domains: Metallo-beta-lactamase superfamily

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand JXF 2 x JXF
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P212121
Unit cell:
a: 39.14Å b: 79.05Å c: 134.28Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.126 0.124 0.16
Expression system: Escherichia coli BL21(DE3)

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