SMTL ID : 6s0c.1

Crystal structure of methionine gamma-lyase from Citrobacter freundii modified by dimethylthiosulfinate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-tetramer

Ligands

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 11 residues within 4Å: Chain A: F.9, P.191, Y.192, C.193, Q.194, Q.195, Q.303, R.304, Q.305, M.306, S.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.303, A:S.307 PGE.3: 11 residues within 4Å: Chain B: F.9, P.191, Y.192, C.193, Q.194, Q.195, Q.303, R.304, Q.305, M.306, S.307 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.303, B:S.307 PGE.5: 11 residues within 4Å: Chain C: F.9, P.191, Y.192, C.193, Q.194, Q.195, Q.303, R.304, Q.305, M.306, S.307 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.303, C:S.307 PGE.7: 11 residues within 4Å: Chain D: F.9, P.191, Y.192, C.193, Q.194, Q.195, Q.303, R.304, Q.305, M.306, S.307 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.303, D:S.307

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

PLP.2: 14 residues within 4Å: Chain A: S.87, G.88, I.89, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, G.220 Chain C: Y.58, R.60 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.113, A:T.187, A:F.188, A:K.210 Hydrogen bonds: A:G.88, A:I.89, A:T.187, A:S.207, A:T.209, A:K.210, A:G.220, C:Y.58 Salt bridges: A:K.210, C:R.60 pi-Stacking: A:Y.113 PLP.4: 14 residues within 4Å: Chain B: S.87, G.88, I.89, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, G.220 Chain D: Y.58, R.60 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Y.113, B:T.187, B:F.188, B:K.210 Hydrogen bonds: B:G.88, B:I.89, B:T.187, B:S.207, B:T.209, B:K.210, B:G.220, D:Y.58 Salt bridges: B:K.210, D:R.60 pi-Stacking: B:Y.113 PLP.6: 14 residues within 4Å: Chain A: Y.58, R.60 Chain C: S.87, G.88, I.89, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, G.220 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.113, C:T.187, C:F.188, C:K.210 Hydrogen bonds: C:G.88, C:I.89, C:S.207, C:G.220 Water bridges: C:E.156 Salt bridges: C:K.210, A:R.60 pi-Stacking: C:Y.113 PLP.8: 14 residues within 4Å: Chain B: Y.58, R.60 Chain D: S.87, G.88, I.89, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, G.220 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.113, D:T.187, D:F.188, D:K.210 Hydrogen bonds: D:G.88, D:I.89, D:S.207, D:G.220 Water bridges: D:E.156 Salt bridges: D:K.210, B:R.60 pi-Stacking: D:Y.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Revtovich, S. et al., Sulfoxides of sulfur-containing amino acids are suicide substrates of Citrobacter freundii methionine gamma-lyase. Structural bases of the enzyme inactivation. Biochimie (2020)

Release Date

2020-04-22

Peptides

Cystathionine gamma-synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Cystathionine gamma-synthase

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