SMTL ID : 5zj7.1

Crystal structure of NDM-1 in complex with D-captopril derivative CY22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.96 Å

Oligo State

monomer

Ligands

1 x 9DU: (2R)-2-methyl-N-(phenylmethyl)-3-sulfanyl-propanamide(Non-covalent)

9DU.1: 12 residues within 4Å: Chain A: M.39, W.65, H.94, D.96, H.161, C.180, N.192, G.194, D.195, H.222 Ligands: ZN.7, ZN.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.65, A:N.192

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

EDO.2: 4 residues within 4Å: Chain A: G.209, R.228, I.231, T.232 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.228 Water bridges: A:A.210, A:R.228 EDO.3: 7 residues within 4Å: Chain A: K.153, G.169, I.170, D.171, T.173, I.175, F.212 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.170, A:T.173, A:I.175, A:I.175 EDO.4: 3 residues within 4Å: Chain A: D.67, D.102, A.103 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.67 EDO.5: 2 residues within 4Å: Chain A: E.142, T.145 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.134 EDO.6: 8 residues within 4Å: Chain A: H.92, A.93, H.94, L.120, E.124, T.162, D.164, D.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.93, A:A.93 Water bridges: A:S.163

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: 9DU.1, ZN.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161 ZN.8: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: 9DU.1, ZN.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:C.180, A:H.222

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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