SMTL ID : 3mkj.1

Methionine gamma-lyase from Citrobacter freundii with pyridoximine-5'-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x PZP: [5-hydroxy-4-(iminomethyl)-6-methyl-pyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

PZP.1: 13 residues within 4Å: Chain A: S.87, G.88, I.89, I.92, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, G.220 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.188 Hydrogen bonds: A:G.88, A:I.89, A:T.187, A:S.207, A:T.209, A:K.210 Water bridges: A:E.156, A:N.160 pi-Stacking: A:Y.113 PZP.2: 13 residues within 4Å: Chain B: S.87, G.88, I.89, I.92, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, G.220 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.188 Hydrogen bonds: B:G.88, B:I.89, B:T.187, B:S.207, B:T.209, B:K.210 Water bridges: B:E.156, B:N.160 pi-Stacking: B:Y.113 PZP.3: 13 residues within 4Å: Chain C: S.87, G.88, I.89, I.92, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, G.220 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.188 Hydrogen bonds: C:G.88, C:I.89, C:S.207, C:K.210 Water bridges: C:E.156, C:E.156, C:N.160 pi-Stacking: C:Y.113 PZP.4: 13 residues within 4Å: Chain D: S.87, G.88, I.89, I.92, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, G.220 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.188 Hydrogen bonds: D:G.88, D:I.89, D:S.207, D:K.210 Water bridges: D:E.156, D:E.156, D:N.160 pi-Stacking: D:Y.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ronda, L. et al., Exploring methionine gamma-lyase structure-function relationship via microspectrophotometry and X-ray crystallography. Biochim.Biophys.Acta (2011)

Release Date

2010-08-11

Peptides

Methionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Methionine gamma-lyase

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