SMTL ID : 6vue.1

wild-type choline TMA lyase in complex with 1-methyl-1,2,3,6-tetrahydropyridin-3-ol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: S.715, M.717, A.718 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.715 Water bridges: A:N.719 NA.3: 3 residues within 4Å: Chain B: S.715, M.717, A.718 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.715, B:N.719

2 x RP7: (3S)-1-methyl-1,2,3,6-tetrahydropyridin-3-ol(Non-covalent)

RP7.2: 14 residues within 4Å: Chain A: Y.177, D.185, T.303, G.304, F.358, F.364, M.456, G.457, C.458, E.460, T.471, Y.475, L.667, I.669 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.358, A:F.364, A:F.364, A:I.669 Hydrogen bonds: A:C.458, A:E.460 Salt bridges: A:D.185, A:E.460 RP7.4: 14 residues within 4Å: Chain B: Y.177, D.185, T.303, G.304, F.358, F.364, M.456, G.457, C.458, E.460, T.471, Y.475, L.667, I.669 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.358, B:F.364, B:F.364, B:I.669 Hydrogen bonds: B:C.458, B:E.460 Salt bridges: B:D.185, B:E.460

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bollenbach, M. et al., Discovery of a Cyclic Choline Analog That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria. Acs Med.Chem.Lett. (2020)

Release Date

2020-11-04

Peptides

Choline trimethylamine-lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Choline trimethylamine-lyase