SMTL ID : 6ex7.1 (1 other biounit)

Crystal structure of NDM-1 metallo-beta-lactamase in complex with Cd ions and a hydrolyzed beta-lactam ligand - new refinement

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 7 residues within 4Å: Chain A: H.93, H.95, D.97, H.162, C.181 Ligands: CD.2, UNL.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.93, A:H.95, A:H.162 CD.2: 5 residues within 4Å: Chain A: D.97, C.181, H.223 Ligands: CD.1, UNL.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.97, A:C.181, A:H.223 CD.3: 2 residues within 4Å: Chain A: E.125, D.196 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.125, A:E.125, A:D.196, H2O.1, H2O.3 CD.7: 1 residues within 4Å: Chain A: E.200 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.200, A:E.200, H2O.2

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

CL.4: 4 residues within 4Å: Chain A: F.213, P.214, K.215, A.216 Ligand excluded by PLIP

1 x UNL: UNKNOWN LIGAND

UNL.5: 11 residues within 4Å: Chain A: H.95, D.97, H.162, C.181, K.184, L.191, G.192, N.193, H.223 Ligands: CD.1, CD.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.193, A:N.193 Salt bridges: A:H.95, A:H.162, A:H.162, A:K.184, A:H.223

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

PG4.6: 3 residues within 4Å: Chain A: A.188, K.189, S.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.189

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

2017-12-13

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase type 2

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