SMTL ID : 5dx5.1

Crystal structure of methionine gamma-lyase from Clostridium sporogenes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 17 residues within 4Å: Chain A: S.87, G.88, M.89, I.92, Y.113, N.160, D.187, T.189, F.190, S.209, T.211, K.212, A.222, L.342 Chain B: Y.58, R.60 Ligands: CL.2 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.190, A:K.212 Hydrogen bonds: A:G.88, A:M.89, A:T.189, A:S.209, A:S.209, A:T.211, A:K.212 Water bridges: A:E.156 Salt bridges: A:K.212, B:R.60 pi-Stacking: A:Y.113 PLP.3: 17 residues within 4Å: Chain A: Y.58, R.60 Chain B: S.87, G.88, M.89, Y.113, E.156, N.160, D.187, T.189, F.190, S.209, T.211, K.212, A.222, L.342 Ligands: CL.4 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:Y.58, B:S.87, B:G.88, B:M.89, B:N.160 Salt bridges: A:R.60, B:K.212 Hydrophobic interactions: B:Y.113, B:K.212 Water bridges: B:E.156 pi-Stacking: B:Y.113 PLP.6: 17 residues within 4Å: Chain C: S.87, G.88, M.89, I.92, Y.113, N.160, D.187, T.189, F.190, S.209, T.211, K.212, A.222, L.342 Chain D: Y.58, R.60 Ligands: CL.7 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.190, C:K.212 Hydrogen bonds: C:G.88, C:M.89, C:S.209, C:S.209, D:Y.58 Water bridges: C:T.116 Salt bridges: C:K.212, D:R.60 pi-Stacking: C:Y.113 PLP.8: 17 residues within 4Å: Chain C: Y.58, R.60 Chain D: S.87, G.88, M.89, Y.113, E.156, N.160, D.187, T.189, F.190, S.209, T.211, K.212, A.222, L.342 Ligands: CL.9 13 PLIP interactions: 3 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:Y.58, C:Y.58, D:S.87, D:G.88, D:M.89, D:N.160, D:T.189, D:T.211 Salt bridges: C:R.60, D:K.212 Hydrophobic interactions: D:Y.113, D:K.212 pi-Stacking: D:Y.113

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: Y.113 Ligands: PLP.1 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain B: Y.113, K.212, S.341, L.342, R.376 Ligands: PLP.3 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain C: Y.113 Ligands: PLP.6 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain D: Y.113, K.212, S.341, L.342, R.376 Ligands: PLP.8 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain B: G.216, H.217, G.218, D.344, S.345, E.346 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.344, B:S.345 NA.10: 6 residues within 4Å: Chain D: G.216, H.217, G.218, D.344, S.345, E.346 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.344, D:S.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Revtovich, S. et al., Structure of methionine gamma-lyase from Clostridium sporogenes. Acta Crystallogr.,Sect.F (2016)

Release Date

2016-01-13

Peptides

Methionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Methionine gamma-lyase