SMTL ID : 5zj1.1

Crystal structure of NDM-1 in complex with D-captopril derivative CYT-14

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.96 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.92, H.94, H.161, C.180 Ligands: ZN.2, YT4.3 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, YT4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:C.180, A:H.222

1 x YT4: methyl (2R)-2-(phenylmethoxycarbonylamino)-3-sulfanyl-propanoate(Non-covalent)

YT4.3: 14 residues within 4Å: Chain A: M.39, F.42, V.45, W.65, H.94, Q.95, D.96, H.161, C.180, G.191, N.192, H.222 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.42 Hydrogen bonds: A:Q.95, A:D.96, A:N.192

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

EDO.4: 8 residues within 4Å: Chain A: K.153, G.169, I.170, D.171, T.173, I.175, K.214, A.215 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.214 EDO.5: 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:A.210 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, A:D.195 EDO.7: 2 residues within 4Å: Chain A: E.142, T.145 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.142 EDO.8: 3 residues within 4Å: Chain A: D.67, D.102, A.103 No protein-ligand interaction detected (PLIP)

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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