SMTL ID : 5zgx.1

Crystal structure of NDM-1 at pH7.5 (Succinate) with 1 molecule per asymmetric unit

Coordinates

PDB Format Compare

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.92, H.94, D.96, H.161, C.180 Ligands: ZN.2, EDO.7, OH.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.92, A:H.94, A:H.161, OH.9 ZN.2: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: ZN.1, OH.9 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.9

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

EDO.3: 9 residues within 4Å: Chain A: H.92, A.93, H.94, L.120, E.124, T.162, S.163, D.164, D.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.93, A:A.93 Water bridges: A:S.163, A:S.163 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: 7 residues within 4Å: Chain A: K.153, G.169, I.170, D.171, T.173, I.175, F.212 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.153, A:I.170, A:D.171, A:D.171, A:T.173, A:I.175, A:I.175 EDO.6: 3 residues within 4Å: Chain A: L.37, T.66, Q.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.95, A:Q.95 EDO.7: 6 residues within 4Å: Chain A: W.65, H.94, D.96, N.192 Ligands: ZN.1, OH.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.96, A:N.192 Water bridges: A:N.192 EDO.8: 3 residues within 4Å: Chain A: A.229, T.232, H.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.232 Water bridges: A:H.233

1 x OH: HYDROXIDE ION(Non-covalent)

OH.9: 8 residues within 4Å: Chain A: H.92, H.94, D.96, H.161, C.180 Ligands: ZN.1, ZN.2, EDO.7 No protein-ligand interaction detected (PLIP)

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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