SMTL ID : 5nbk.2 (1 other biounit)

NDM-1 metallo-beta-lactamase: a parsimonious interpretation of the diffraction data

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.93, H.95, D.97, H.162, C.181 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.93, A:H.95, A:H.162, H2O.2 ZN.2: 5 residues within 4Å: Chain A: D.97, H.162, C.181, H.223 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.97, A:C.181, A:H.223, H2O.2, H2O.2

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 8 residues within 4Å: Chain A: K.154, G.170, I.171, D.172, G.173, T.174, I.176, F.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.172 Water bridges: A:A.216 PG4.4: 8 residues within 4Å: Chain A: D.16, Q.17, F.24, R.25, Q.26, W.32, R.54, E.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.26, A:R.54

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: H.234, R.237 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raczynska, J.E. et al., A close look onto structural models and primary ligands of metallo-beta-lactamases. Drug Resist. Updat. (2018)

Release Date

2018-10-03

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Metallo-beta-lactamase type 2

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