SMTL ID : 5n0i.2 (1 other biounit)

Crystal structure of NDM-1 in complex with beta-mercaptoethanol - new refinement

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: ZN.2, BME.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:C.180, A:H.222 ZN.2: 5 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: ZN.1, BME.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.3: 11 residues within 4Å: Chain A: M.39, W.65, H.92, H.94, D.96, H.161, C.180, H.222 Ligands: ZN.1, ZN.2, GOL.4 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: H.94, H.161, G.191, N.192, L.193 Ligands: BME.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.94, A:N.192, A:L.193, A:G.194 Water bridges: A:H.161

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

CL.5: 4 residues within 4Å: Chain A: F.212, P.213, K.214, A.215 Ligand excluded by PLIP

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

PG4.6: 2 residues within 4Å: Chain A: L.37, D.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.38

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

2017-04-05

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Metallo-beta-lactamase type 2

Related Entries With Identical Sequence