SMTL ID : 5zr8.1

Crystal Structure Of NDM-1 Metallo-beta-lactamase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.96, H.98, H.165 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.96, A:H.98, A:H.165, H2O.8 ZN.2: 4 residues within 4Å: Chain A: D.100, C.184, H.226 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.100, A:C.184, A:H.226, H2O.8 ZN.3: 3 residues within 4Å: Chain A: E.128, D.199 Chain B: E.203 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:E.203, B:E.203, A:E.128, A:E.128, A:D.199 ZN.7: 3 residues within 4Å: Chain A: E.203 Chain B: E.128, D.199 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.128, B:E.128, B:D.199, A:E.203, H2O.16 ZN.8: 4 residues within 4Å: Chain B: H.96, H.98, H.165 Ligands: ZN.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.96, B:H.98, B:H.165, H2O.18 ZN.9: 4 residues within 4Å: Chain B: D.100, C.184, H.226 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.100, B:C.184, B:H.226, H2O.18

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: R.210, T.236, R.240 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.240 Salt bridges: A:R.210, A:R.240 SO4.5: 1 residues within 4Å: Chain A: R.232 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.232 SO4.6: 4 residues within 4Å: Chain A: K.187, A.191, K.192, S.193 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.192, A:S.193, A:S.193 Water bridges: A:K.187 Salt bridges: A:K.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wachino, J., Crystal Structure Of NDM-1 Metallo-beta-lactamase. To Be Published

Release Date

2019-04-24

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Beta-lactamase

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