SMTL ID : 6m2y.1

Crystal structure of a formolase, BFD variant M6 from Pseudomonas putida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 19 residues within 4Å: Chain A: T.377, S.378, G.401, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, M.460 Chain D: N.23, P.24, E.47, N.77 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.403, A:Y.458 Hydrogen bonds: A:T.377, A:T.377, A:S.378, A:G.401, A:L.403, A:D.428, A:G.429, A:S.430, A:Y.433, A:N.455, A:N.455, A:G.459, A:M.460 Water bridges: A:D.428, A:D.428 TPP.3: 19 residues within 4Å: Chain B: T.377, S.378, G.401, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, M.460 Chain C: N.23, P.24, E.47, N.77 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.403, B:Y.458 Hydrogen bonds: B:T.377, B:T.377, B:S.378, B:G.401, B:L.403, B:D.428, B:G.429, B:S.430, B:Y.433, B:N.455, B:N.455, B:G.459, B:M.460 Water bridges: B:D.428, B:D.428 TPP.5: 19 residues within 4Å: Chain B: N.23, P.24, E.47, N.77 Chain C: T.377, S.378, G.401, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, M.460 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.403, C:Y.458 Hydrogen bonds: C:T.377, C:T.377, C:T.377, C:S.378, C:G.401, C:L.403, C:G.429, C:S.430, C:N.455, C:G.459, C:M.460 Water bridges: C:D.428, C:D.428 TPP.7: 19 residues within 4Å: Chain A: N.23, P.24, E.47, N.77 Chain D: T.377, S.378, G.401, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, M.460 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.403, D:Y.458 Hydrogen bonds: D:T.377, D:T.377, D:T.377, D:S.378, D:G.401, D:L.403, D:G.429, D:S.430, D:N.455, D:G.459, D:M.460 Water bridges: D:D.428, D:D.428

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.5 MG.4: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.428, B:T.457, H2O.22 MG.6: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.39 MG.8: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, T. et al., Totally atom-economical synthesis of lactic acid from formaldehyde: combined bio-carboligation and chemo-rearrangement without the isolation of intermediate. Green Chem (2020)

Release Date

2021-03-03

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Benzoylformate decarboxylase