SMTL ID : 6jkb.1

Crystal structure of metallo-beta-lactamse, NDM-1, in complex with hydrolyzed ampicillin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.98, C.182, H.224 Ligands: ZZ7.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.98, A:C.182, A:H.224 ZN.2: 4 residues within 4Å: Chain A: H.94, H.96, H.163 Ligands: ZZ7.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.94, A:H.96, A:H.163 ZN.4: 4 residues within 4Å: Chain B: H.94, H.96, H.163 Ligands: ZZ7.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.94, B:H.96, B:H.163 ZN.5: 5 residues within 4Å: Chain B: D.98, C.182, S.223, H.224 Ligands: ZZ7.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.98, B:C.182, B:H.224

2 x ZZ7: (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

ZZ7.3: 14 residues within 4Å: Chain A: W.67, H.94, H.96, Q.97, D.98, E.126, H.163, C.182, K.185, G.193, N.194, H.224 Ligands: ZN.1, ZN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.96, A:Q.97 Hydrogen bonds: A:Q.97, A:D.98, A:L.192, A:N.194, A:N.194 Salt bridges: A:H.94, A:H.96, A:H.163, A:H.163, A:K.185, A:H.224 ZZ7.6: 14 residues within 4Å: Chain B: W.67, H.94, H.96, Q.97, D.98, H.163, C.182, K.185, L.192, G.193, N.194, H.224 Ligands: ZN.4, ZN.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:N.194 Hydrogen bonds: B:H.96, B:G.193, B:N.194, B:N.194 Salt bridges: B:H.94, B:H.96, B:H.163, B:H.163, B:K.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kamo, T. et al., Identification of the Inhibitory Compounds for Metallo-beta-lactamases and Structural Analysis of the Binding Modes. Chem Pharm Bull (Tokyo) (2021)

Release Date

2020-03-25

Peptides

Metallo-beta-lactamase type 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metallo-beta-lactamase type 2