SMTL ID : 8wkr.1

Crystal structure of O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum in the open form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x LLP: (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid(Covalent)

LLP.1: 19 residues within 4Å: Chain A: T.108, G.109, S.110, Y.134, D.206, T.208, F.209, S.228, A.229, T.230, F.232, I.233, G.234, G.235, M.240, G.241, N.391, V.392, A.393 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.134, A:T.208, A:V.392, A:A.393 Hydrogen bonds: A:G.109, A:S.110, A:S.110, A:S.228, A:S.228, A:T.230, A:T.230, A:G.234, A:G.235 Water bridges: A:S.110, A:S.110, A:F.232, A:R.315, A:V.392 LLP.3: 19 residues within 4Å: Chain B: T.108, G.109, S.110, I.113, Y.134, D.206, T.208, F.209, S.228, A.229, T.230, F.232, I.233, G.234, G.235, G.241, N.391, V.392, A.393 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.208, B:A.393 Hydrogen bonds: B:G.109, B:S.110, B:S.110, B:T.137, B:S.228, B:S.228, B:T.230, B:G.234, B:G.235 Water bridges: B:S.110, B:S.110, B:D.206, B:I.233, B:V.392 LLP.4: 19 residues within 4Å: Chain C: T.108, G.109, S.110, Y.134, D.206, T.208, F.209, S.228, A.229, T.230, F.232, I.233, G.234, G.235, M.240, G.241, N.391, V.392, A.393 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:Y.134, C:T.208, C:V.392, C:A.393 Hydrogen bonds: C:G.109, C:S.110, C:S.110, C:T.137, C:S.228, C:S.228, C:T.230, C:T.230, C:G.234, C:G.235 Water bridges: C:S.110, C:S.110, C:Y.134, C:D.206, C:I.233 pi-Stacking: C:Y.134 LLP.6: 20 residues within 4Å: Chain D: T.108, G.109, S.110, I.113, Y.134, D.206, T.208, F.209, S.228, A.229, T.230, F.232, I.233, G.234, G.235, M.240, G.241, N.391, V.392, A.393 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:T.208, D:F.209, D:V.392, D:A.393 Hydrogen bonds: D:G.109, D:S.110, D:S.110, D:S.228, D:S.228, D:T.230, D:G.234, D:G.235 Water bridges: D:T.137, D:I.233 pi-Stacking: D:Y.134

2 x PRO: PROLINE(Non-covalent)

PRO.2: 10 residues within 4Å: Chain A: H.236, Q.307, G.308, S.311, R.315 Chain B: H.236, Q.307, G.308, S.311, R.315 8 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: P.2, P.2, A:S.311, B:H.236, B:S.311 Hydrophobic interactions: A:Q.307 Salt bridges: A:H.236, B:H.236 PRO.5: 10 residues within 4Å: Chain C: H.236, Q.307, G.308, S.311, R.315 Chain D: H.236, Q.307, G.308, S.311, R.315 8 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: C:H.236, C:S.311, D:S.311, P.5, P.5 Salt bridges: C:H.236, D:H.236 Hydrophobic interactions: D:Q.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matoba, Y. et al., Allosteric regulation of an acidophilic O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum. To Be Published

Release Date

2024-02-14

Peptides

L-methionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-methionine gamma-lyase

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