SMTL ID : 6qsi.1

Pseudomonas fluorescens Pf-5 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 23 residues within 4Å: Chain A: S.376, 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, A.460, L.461 Chain B: N.23, P.24, G.25, E.47, H.70, N.77 Ligands: NA.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.433, A:L.461 Hydrogen bonds: A:T.377, A:T.377, A:T.377, A:S.378, A:G.401, A:L.403, A:G.427, A:G.429, A:S.430, A:N.455, A:N.455, A:G.459, A:A.460 Water bridges: A:D.428, A:D.428 TPP.5: 22 residues within 4Å: Chain A: N.23, P.24, G.25, E.47, H.70, N.77 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, A.460, L.461 Ligands: NA.6 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.403, B:Y.433, B:L.461 Hydrogen bonds: B:S.376, B:T.377, B:S.378, B:G.401, B:L.403, B:G.427, B:D.428, B:G.429, B:S.430, B:Y.433, B:N.455, B:G.459, B:A.460, A:H.70 Water bridges: B:D.428, B:D.428

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

NA.2: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: TPP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.455, A:N.455, A:T.457 NA.6: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: TPP.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.428, B:N.455, B:T.457

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: H.46, N.432, Y.433, T.436 Chain B: H.46, N.432, Y.433, T.436 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.432, A:N.432 Water bridges: B:T.436 EDO.4: 7 residues within 4Å: Chain A: W.86, Y.87, H.89, P.276, D.301, E.304, R.307 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.301, A:E.304, A:E.304, A:R.307, A:R.307 Water bridges: A:W.86, A:Y.87, A:D.301, A:G.303 EDO.7: 7 residues within 4Å: Chain B: W.86, Y.87, H.89, P.276, D.301, E.304, R.307 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.304, B:R.307, B:R.307 Water bridges: B:D.301, B:G.303, A:E.107, A:E.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, Z. et al., Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes fromRhodococcus jostiiRHA1 andPseudomonas fluorescensPf-5 Involved in Degradation of Aryl C2Lignin Degradation Fragments. Biochemistry (2019)

Release Date

2020-01-08

Peptides

Benzoylformate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Benzoylformate decarboxylase