SMTL ID : 8y64.1

Crystal structure of open state ferulic acid decarboxylase from Saccharomyces cerevisiae, F397V/I398L/T438P/P441V mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: R.175, P.282, F.283, Y.289, V.290, F.291, L.442 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.175, A:R.175, A:F.283, A:F.283, A:F.291 GOL.2: 8 residues within 4Å: Chain A: P.379, E.380, C.383, A.429, D.430, Q.431, M.432, N.463 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.430, A:N.463 Water bridges: A:E.380, A:D.430, A:D.430 GOL.3: 5 residues within 4Å: Chain A: K.384, D.388, M.432, A.433, F.434 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.384, A:A.433 Water bridges: A:D.388, A:D.388 GOL.4: 4 residues within 4Å: Chain B: K.384, D.388, A.433, F.434 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.384, B:D.388, B:A.433 GOL.5: 8 residues within 4Å: Chain B: T.155, Y.156, I.173, R.175, S.227, S.317, E.325, T.326 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.175, B:R.175, B:S.227, B:S.227, B:S.317, B:S.317 Water bridges: B:T.155, B:I.173 GOL.7: 6 residues within 4Å: Chain A: V.146 Chain B: I.477, K.483, G.484, Y.485, P.486 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.484 Water bridges: B:D.475, B:Y.485

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 8 residues within 4Å: Chain B: P.379, E.380, C.383, A.429, D.430, Q.431, M.432, N.463 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.463 Water bridges: B:D.430

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, X.N. et al., Integrated strategies for engineering ferulic acid decarboxylase with tunnel conformation and substrate pocket for adapting non-natural substrates. Biochem Eng J (2025)

Release Date

2025-01-01

Peptides

Ferulic acid decarboxylase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ferulic acid decarboxylase 1