SMTL ID : 1pg8.1

Crystal Structure of L-methionine alpha-, gamma-lyase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: Y.114, N.161, K.211, V.339, S.340, L.341, R.375 Ligands: PLP.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.161, A:S.340 Water bridges: A:N.161, A:Y.189, A:R.375 Salt bridges: A:K.211, A:R.375 SO4.10: 8 residues within 4Å: Chain B: Y.114, K.211, V.339, S.340, L.341, Q.349, R.375 Ligands: PLP.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.114, B:Y.114, B:S.340, B:Q.349 Water bridges: B:G.115 Salt bridges: B:K.211, B:R.375 SO4.14: 8 residues within 4Å: Chain C: Y.114, N.161, K.211, V.339, S.340, L.341, Q.349, R.375 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.114, C:N.161, C:S.340, C:Q.349 Water bridges: C:K.211, C:K.211, C:R.375, C:R.375 Salt bridges: C:K.211, C:R.375 SO4.18: 7 residues within 4Å: Chain D: Y.114, K.211, V.339, S.340, Q.349, R.375 Ligands: PLP.19 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.340 Salt bridges: D:K.211, D:R.375

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

PLP.2: 16 residues within 4Å: Chain A: S.88, G.89, M.90, I.93, Y.114, D.186, T.188, Y.189, S.208, T.210, K.211, A.221, L.341 Chain C: Y.59, R.61 Ligands: SO4.1 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.114, A:Y.189 Hydrogen bonds: A:S.88, A:G.89, A:M.90, A:Y.114, A:T.188, A:S.208, A:T.210, C:Y.59, C:Y.59 Salt bridges: A:K.211, C:R.61 pi-Stacking: A:Y.114 PLP.11: 15 residues within 4Å: Chain B: S.88, G.89, M.90, Y.114, D.186, T.188, Y.189, S.208, T.210, K.211, A.221, L.341 Chain D: Y.59, R.61 Ligands: SO4.10 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.114, B:Y.189 Hydrogen bonds: B:S.88, B:G.89, B:M.90, B:S.208, B:S.208 Water bridges: B:E.157 Salt bridges: B:K.211, D:R.61 pi-Stacking: B:Y.114 PLP.15: 16 residues within 4Å: Chain A: Y.59, R.61 Chain C: S.88, G.89, M.90, I.93, Y.114, D.186, T.188, Y.189, S.208, T.210, K.211, T.220, A.221, L.341 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain C Salt bridges: A:R.61, C:K.211 Hydrophobic interactions: C:Y.114, C:Y.189, C:K.211 Hydrogen bonds: C:S.88, C:G.89, C:M.90, C:S.208, C:S.208 Water bridges: C:T.117, C:Y.189 pi-Stacking: C:Y.114 PLP.19: 16 residues within 4Å: Chain B: Y.59, R.61 Chain D: S.88, G.89, M.90, I.93, Y.114, D.186, T.188, Y.189, S.208, T.210, K.211, A.221, L.341 Ligands: SO4.18 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.114, D:Y.189 Hydrogen bonds: D:S.88, D:G.89, D:M.90, D:T.188, D:S.208, D:S.208, D:T.210, B:Y.59 Salt bridges: D:K.211, B:R.61 pi-Stacking: D:Y.114

11 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: S.4, K.6, P.8 Chain D: D.385 Ligands: PEG.4 No protein-ligand interaction detected (PLIP) PEG.4: 7 residues within 4Å: Chain A: P.8, T.12, R.13, H.16, H.17 Ligands: PEG.3, PEG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.17 PEG.5: 5 residues within 4Å: Chain A: H.16, H.17, G.18, Y.19 Ligands: PEG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.16, A:Y.19 PEG.6: 5 residues within 4Å: Chain A: D.23, H.24, Y.33, H.57 Chain B: G.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.23, A:H.57 PEG.7: 3 residues within 4Å: Chain A: G.25 Chain B: H.24, P.65 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.23 PEG.8: 7 residues within 4Å: Chain A: A.295, S.296, F.297, P.298, Q.299, Y.300, T.301 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.300, A:T.301, A:T.301 Water bridges: A:L.302 PEG.9: 11 residues within 4Å: Chain A: G.110, N.111, T.112, L.113, V.135, D.136, M.137, F.156, E.157, A.160, H.165 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.110, A:N.111, A:V.135, A:M.137, A:E.157 Water bridges: A:N.111 PEG.12: 9 residues within 4Å: Chain B: G.18, Y.19, H.24, P.30, P.31, V.32, Y.33, P.65, T.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.18 Water bridges: B:D.20 PEG.13: 4 residues within 4Å: Chain B: P.8, R.13, H.16, H.17 No protein-ligand interaction detected (PLIP) PEG.16: 8 residues within 4Å: Chain B: A.11, N.263 Chain C: R.268, N.272, L.380, E.381, D.382, I.383 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.268, C:N.272, C:L.380, C:I.383, B:N.263 PEG.17: 6 residues within 4Å: Chain B: H.16, D.20, P.21 Chain C: Q.333, L.334, S.336 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

?. To Be Published

Release Date

2004-06-08

Peptides

Methionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Methionine gamma-lyase

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