SMTL ID : 6jka.2 (1 other biounit)

Crystal structure of metallo-beta-lactamse, IMP-1, in complex with a thiazole-bearing inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.85, C.162, H.201 Ligands: ZN.2, BQU.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.85, A:C.162, A:H.201 ZN.2: 7 residues within 4Å: Chain A: H.81, H.83, D.85, H.143, C.162 Ligands: ZN.1, BQU.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.81, A:H.83, A:H.143 ZN.4: 4 residues within 4Å: Chain B: D.85, C.162, H.201 Ligands: ZN.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.85, B:C.162, B:H.201, H2O.5, H2O.5 ZN.5: 6 residues within 4Å: Chain B: H.81, H.83, D.85, H.143, C.162 Ligands: ZN.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.81, B:H.83, B:H.143, H2O.5

1 x BQU: 3-[2-azanyl-5-[2-(phenoxymethyl)-1,3-thiazol-4-yl]phenyl]propanoic acid(Non-covalent)

BQU.3: 17 residues within 4Å: Chain A: W.32, H.81, H.83, D.85, H.143, C.162, K.165, P.166, Y.167, G.168, G.170, N.171, H.201, S.202 Chain B: E.203 Ligands: ZN.1, ZN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.165, A:P.166, A:Y.167, A:N.171 Hydrogen bonds: A:H.143, A:N.171 Salt bridges: A:H.81, A:H.83, A:H.143, A:H.201 pi-Stacking: A:W.32, A:W.32, A:H.201

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
B

B
D

Metallo-beta-lactamase type 2

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