SMTL ID : 8wko.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

homo-tetramer

Ligands

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: H.30, F.31, R.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.31, A:R.216 Salt bridges: A:H.30 SO4.2: 8 residues within 4Å: Chain A: Y.134, N.181, A.390, N.391, V.392, T.406, R.426 Ligands: LLP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.134, A:N.181 Salt bridges: A:R.426 SO4.4: 5 residues within 4Å: Chain B: H.37, Q.40, T.41, V.42, R.48 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.37 Salt bridges: B:R.48 SO4.5: 7 residues within 4Å: Chain B: Y.134, A.390, N.391, V.392, T.406, R.426 Ligands: LLP.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.134, B:Y.134, B:N.181 Salt bridges: B:R.426 SO4.6: 4 residues within 4Å: Chain B: H.30, F.31, H.99, R.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.31 Salt bridges: B:R.216 SO4.9: 3 residues within 4Å: Chain C: H.30, F.31, R.216 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.31, C:R.216 Salt bridges: C:H.30 SO4.10: 8 residues within 4Å: Chain C: Y.134, N.181, A.390, N.391, V.392, T.406, R.426 Ligands: LLP.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.181 Salt bridges: C:R.426 SO4.12: 5 residues within 4Å: Chain D: H.37, Q.40, T.41, V.42, R.48 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.48 SO4.13: 7 residues within 4Å: Chain D: Y.134, A.390, N.391, V.392, T.406, R.426 Ligands: LLP.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.134, D:N.181 Salt bridges: D:R.426 SO4.14: 4 residues within 4Å: Chain D: H.30, F.31, H.99, R.216 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.31 Salt bridges: D:R.216

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

LLP.3: 25 residues within 4Å: Chain A: T.108, G.109, S.110, I.113, Y.134, T.137, E.177, N.181, D.206, T.208, F.209, S.228, A.229, T.230, F.232, I.233, G.234, G.235, M.240, N.391, V.392, A.393 Chain C: Y.79, R.81 Ligands: SO4.2 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain C 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:T.137, A:N.181, A:S.228, A:S.228, A:S.228, A:G.234, A:G.235 Salt bridges: C:R.81 LLP.8: 23 residues within 4Å: Chain B: T.108, G.109, S.110, Y.134, T.137, E.177, N.181, D.206, T.208, F.209, S.228, A.229, T.230, F.232, I.233, G.234, G.235, N.391, V.392, A.393 Chain D: Y.79, R.81 Ligands: SO4.5 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.134, B:Y.134, B:T.208, B:V.392, B:A.393 Hydrogen bonds: B:G.109, B:S.110, B:S.110, B:T.137, B:N.181, B:S.228, B:S.228, B:S.228, B:T.230, B:G.234, B:G.235 Salt bridges: D:R.81 LLP.11: 25 residues within 4Å: Chain A: Y.79, R.81 Chain C: T.108, G.109, S.110, I.113, Y.134, T.137, E.177, N.181, D.206, T.208, F.209, S.228, A.229, T.230, F.232, I.233, G.234, G.235, M.240, N.391, V.392, A.393 Ligands: SO4.10 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain A 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:N.181, C:S.228, C:S.228, C:S.228, C:T.230, C:G.234, C:G.235, A:Y.79 Salt bridges: A:R.81 LLP.16: 23 residues within 4Å: Chain B: Y.79, R.81 Chain D: T.108, G.109, S.110, Y.134, T.137, E.177, N.181, D.206, T.208, F.209, S.228, A.229, T.230, F.232, I.233, G.234, G.235, N.391, V.392, A.393 Ligands: SO4.13 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.134, D:Y.134, D:T.208, D:V.392, D:A.393 Hydrogen bonds: D:G.109, D:S.110, D:S.110, D:N.181, D:T.208, D:S.228, D:S.228, D:S.228, D:G.234, D:G.235, B:Y.79 Salt bridges: B:R.81

2 x PRO: PROLINE(Non-covalent)

PRO.7: 9 residues within 4Å: Chain A: H.236, Q.307, S.311, R.315 Chain B: H.236, Q.307, G.308, S.311, R.315 8 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions, 3 interactions with chain A Hydrophobic interactions: B:Q.307 Hydrogen bonds: B:S.311, P.7, P.7, A:H.236, A:S.311 Salt bridges: B:H.236, A:H.236 PRO.15: 9 residues within 4Å: Chain C: H.236, Q.307, S.311, R.315 Chain D: H.236, Q.307, G.308, S.311, R.315 8 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: P.15, P.15, C:H.236, C:S.311, D:S.311 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
A

D
B

L-methionine gamma-lyase

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