SMTL ID : 6qp3.1 (1 other biounit)

Crystal structure of the PLP-bound C-S lyase from Bacillus subtilis (strain 168)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: V.34, A.35, Y.119, N.171, E.351, R.365 Ligands: PLP.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.119 Hydrogen bonds: A:A.35, A:N.171, A:E.351 Salt bridges: A:K.234, A:R.365 ACT.3: 8 residues within 4Å: Chain B: V.34, A.35, Y.119, N.171, K.234, E.351, R.365 Ligands: PLP.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.34, B:Y.119 Hydrogen bonds: B:A.35, B:N.171, B:E.351 Salt bridges: B:K.234, B:R.365

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.2: 13 residues within 4Å: Chain A: G.93, V.94, V.95, Y.119, C.167, N.171, D.199, I.201, H.202, K.234, S.244 Chain B: Y.60 Ligands: ACT.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.119, A:I.201, A:I.201, A:K.234 Hydrogen bonds: A:V.94, A:V.95, A:N.171, A:H.202 Salt bridges: A:K.234 pi-Stacking: A:Y.119 PLP.4: 13 residues within 4Å: Chain A: Y.60 Chain B: G.93, V.94, V.95, Y.119, C.167, N.171, D.199, I.201, H.202, S.233, K.234 Ligands: ACT.3 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.119, B:I.201, B:I.201, B:K.234 Hydrogen bonds: B:V.94, B:V.95, B:N.171, B:H.202, B:S.233, A:Y.60, A:Y.60 pi-Stacking: B:Y.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudden, M. et al., The molecular basis of thioalcohol production in human body odour. Sci Rep (2020)

Release Date

2020-03-04

Peptides

Cystathionine beta-lyase PatB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Cystathionine beta-lyase PatB

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