SMTL ID : 5xp6.1

native structure of NDM-1 crystallized at pH5.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.95 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: H.93, H.95, D.97, H.162, C.181 Ligands: ZN.2, OH.3, SIN.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.93, A:H.95, A:H.162, OH.3 ZN.2: 6 residues within 4Å: Chain A: D.97, C.181, H.223 Ligands: ZN.1, OH.3, SIN.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.97, A:C.181, A:H.223, OH.3

1 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 8 residues within 4Å: Chain A: H.93, H.95, D.97, H.162, C.181 Ligands: ZN.1, ZN.2, SIN.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.97, A:D.97

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: L.38, T.67, Q.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.96, A:Q.96 EDO.5: 3 residues within 4Å: Chain A: D.68, D.103, A.104 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: M.40, W.66, Q.96 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.96, A:Q.96 EDO.7: 4 residues within 4Å: Chain A: G.210, R.229, I.232, T.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.229 Water bridges: A:A.211 EDO.8: 5 residues within 4Å: Chain A: W.66, T.67, D.68, Q.96, G.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.68, A:D.68 Water bridges: A:D.69

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.9: 9 residues within 4Å: Chain A: M.40, D.97, H.162, C.181, N.193, H.223 Ligands: ZN.1, ZN.2, OH.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.193, A:N.193 Water bridges: A:K.184 Salt bridges: A:H.162, A:K.184, A:H.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, R. et al., Bismuth antimicrobial drugs serve as broad-spectrum metallo-beta-lactamase inhibitors. Nat Commun (2018)

Release Date

2018-03-07

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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