SMTL ID : 5faw.1

T502A mutant of choline TMA-lyase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: S.715, M.717, A.718, N.719 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.719 Water bridges: A:S.715, A:L.756 NA.7: 3 residues within 4Å: Chain A: L.210, E.211, L.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.210

6 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 3 residues within 4Å: Chain A: R.538, R.541, L.658 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.658 Hydrogen bonds: A:R.538 Water bridges: A:R.541, A:L.658 Salt bridges: A:R.541 MLI.3: 4 residues within 4Å: Chain A: R.207, L.210, K.228, I.231 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.228, A:K.228 Salt bridges: A:R.207, A:K.228 MLI.4: 4 residues within 4Å: Chain A: I.56, K.71, R.74, Y.75 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.56 Water bridges: A:R.74, A:R.74 Salt bridges: A:K.71, A:R.74, A:R.74 MLI.5: 7 residues within 4Å: Chain A: R.17, G.18, S.19, H.20, R.259, Y.330, E.331 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.18, A:S.19, A:H.20 Water bridges: A:S.19, A:S.19 Salt bridges: A:H.20, A:H.20, A:R.259 MLI.6: 5 residues within 4Å: Chain A: H.488, D.504, L.505, S.506, A.604 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:L.505 Water bridges: A:S.506, A:N.607, A:N.607, A:K.611, A:K.611, A:K.611 Salt bridges: A:H.488, A:H.488, A:K.611 MLI.9: 4 residues within 4Å: Chain B: S.19, H.20, M.21, G.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.21, B:G.22 Water bridges: B:S.19, B:S.19

2 x CHT: CHOLINE ION(Non-covalent)

CHT.8: 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, A.471, Y.475, L.667, I.669 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.458, A:E.460 Salt bridges: A:D.185, A:E.460 CHT.10: 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, A.471, Y.475, L.667, I.669 4 PLIP interactions: 4 interactions with chain B 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

Bodea, S. et al., Molecular Basis of C-N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase. Cell Chem Biol (2016)

Release Date

2016-09-28

Peptides

Choline trimethylamine-lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Choline trimethylamine-lyase