SMTL ID : 5zgw.1

Crystal structure of NDM-1 at pH7.5 with 1 molecule per asymmetric unit (crystallized at succinate pH5.5 and soaked at succinate pH7.5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.95 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.92, H.94, D.96, H.161, C.180 Ligands: ZN.2, OH.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.92, A:H.94, A:H.161, OH.3 ZN.2: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: ZN.1, OH.3 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.96, A:C.180, A:H.222, H2O.1, OH.3

1 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 8 residues within 4Å: Chain A: H.92, H.94, D.96, H.161, C.180, H.222 Ligands: ZN.1, ZN.2 No protein-ligand interaction detected (PLIP)

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

EDO.4: 3 residues within 4Å: Chain A: L.37, M.39, Q.95 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.95 EDO.5: 3 residues within 4Å: Chain A: A.229, T.232, H.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.232 EDO.6: 5 residues within 4Å: Chain A: P.143, A.146, N.148, F.149, G.150 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.143, A:N.148, A:F.149, A:G.150 Water bridges: A:F.149, A:G.150 EDO.7: 4 residues within 4Å: Chain A: G.209, R.228, I.231, T.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.228 EDO.8: 9 residues within 4Å: Chain A: H.92, A.93, H.94, L.120, E.124, T.162, S.163, D.164, D.195 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.93, A:A.93 Water bridges: A:S.163, A:S.163, A:S.163, A:S.163 EDO.9: 9 residues within 4Å: Chain A: K.153, G.169, I.170, D.171, T.173, I.175, F.212, K.214, A.215 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.171, A:D.171 Water bridges: A:A.215

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: W.65, T.66, D.67, Q.95, G.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.67 Water bridges: A:T.66, A:D.68, A:G.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1. Antimicrob. Agents Chemother. (2018)

Release Date

2018-08-22

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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