SMTL ID : 5zj8.1

Crystal structure of NDM-1 in complex with D-captopril derivative CY32

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.96 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: ZN.2, 9DC.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161 ZN.2: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: ZN.1, 9DC.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:C.180, A:H.222

1 x 9DC: (2S)-2,3-disulfanylpropan-1-ol(Non-covalent)

9DC.3: 10 residues within 4Å: Chain A: M.39, W.65, H.94, D.96, H.161, C.180, N.192, H.222 Ligands: ZN.1, ZN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.192 Water bridges: A:Q.95

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

EDO.4: 4 residues within 4Å: Chain A: G.209, R.228, I.231, T.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.228 Water bridges: A:R.228 EDO.5: 8 residues within 4Å: Chain A: H.92, A.93, H.94, L.120, E.124, T.162, D.164, D.195 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.93, A:A.93 Water bridges: A:Q.123, A:E.124, A:E.124, A:E.124, A:S.163 EDO.6: 2 residues within 4Å: Chain A: E.142, T.145 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.134 EDO.7: 3 residues within 4Å: Chain A: D.67, D.102, A.103 No protein-ligand interaction detected (PLIP) EDO.8: 7 residues within 4Å: Chain A: K.153, G.169, I.170, D.171, T.173, I.175, A.215 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.170, A:I.175 Water bridges: A:K.153, A:D.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Crystal structure of NDM-1. to be published

Release Date

2019-03-20

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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