SMTL ID : 1e5f.1

METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 17 residues within 4Å: Chain A: S.85, G.86, M.87, I.90, Y.111, E.154, N.158, D.184, T.186, S.206, T.208, K.209, V.218, A.219 Chain B: Y.56, R.58 Ligands: SO4.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.111, A:Y.111 Hydrogen bonds: A:G.86, A:M.87, A:N.158, A:S.206, A:S.206, B:Y.56 Water bridges: A:T.114 Salt bridges: A:K.209, B:R.58 PLP.6: 16 residues within 4Å: Chain A: Y.56, R.58 Chain B: S.85, G.86, M.87, Y.111, E.154, N.158, D.184, T.186, F.187, S.206, T.208, K.209, A.219 Ligands: SO4.7 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.111 Hydrogen bonds: B:G.86, B:M.87, B:N.158, B:S.206, B:S.206, B:T.208, B:K.209, A:Y.56 Water bridges: B:T.114 Salt bridges: B:K.209, A:R.58 pi-Stacking: B:Y.111 PLP.10: 17 residues within 4Å: Chain C: S.85, G.86, M.87, I.90, Y.111, E.154, N.158, D.184, T.186, S.206, T.208, K.209, V.218, A.219 Chain D: Y.56, R.58 Ligands: SO4.11 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.111, C:Y.111 Hydrogen bonds: C:G.86, C:M.87, C:N.158, C:T.186, C:S.206, C:S.206, C:T.208 Water bridges: C:E.154 Salt bridges: C:K.209, D:R.58 PLP.15: 16 residues within 4Å: Chain C: Y.56, R.58 Chain D: S.85, G.86, M.87, Y.111, E.154, N.158, D.184, T.186, F.187, S.206, T.208, K.209, A.219 Ligands: SO4.16 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.111 Hydrogen bonds: D:G.86, D:M.87, D:N.158, D:T.186, D:S.206, D:S.206, D:K.209 Water bridges: D:D.184 Salt bridges: D:K.209, C:R.58 pi-Stacking: D:Y.111

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

SO4.2: 9 residues within 4Å: Chain A: Y.111, N.158, K.209, V.337, S.338, L.339, T.353, R.373 Ligands: PLP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.111, A:N.158, A:S.338 Water bridges: A:Y.111 Salt bridges: A:K.209, A:R.373 SO4.3: 3 residues within 4Å: Chain A: H.298, K.302, Y.308 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.298, A:K.302 SO4.4: 2 residues within 4Å: Chain A: K.279, K.286 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.287 Salt bridges: A:K.279, A:K.286 SO4.7: 9 residues within 4Å: Chain B: Y.111, N.158, K.209, V.337, S.338, L.339, T.353, R.373 Ligands: PLP.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.111, B:N.158, B:S.338, B:S.338 Salt bridges: B:K.209, B:R.373 SO4.8: 2 residues within 4Å: Chain B: E.177, G.178 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.178 Water bridges: B:V.179, B:V.179, B:V.179 SO4.9: 5 residues within 4Å: Chain B: E.276, K.279, F.292, E.293, D.294 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.293, B:D.294, B:D.294 Salt bridges: B:K.279 SO4.11: 9 residues within 4Å: Chain C: Y.111, N.158, K.209, V.337, S.338, L.339, T.353, R.373 Ligands: PLP.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.158, C:S.338 Water bridges: C:Y.111 Salt bridges: C:K.209, C:R.373 SO4.12: 3 residues within 4Å: Chain C: H.298, K.302, Y.308 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.308 Salt bridges: C:H.298, C:K.302 SO4.13: 2 residues within 4Å: Chain C: K.279, K.286 3 PLIP interactions: 3 interactions with chain C Water bridges: C:V.287 Salt bridges: C:K.279, C:K.286 SO4.16: 9 residues within 4Å: Chain D: Y.111, N.158, K.209, V.337, S.338, L.339, T.353, R.373 Ligands: PLP.15 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.111, D:Y.111, D:N.158, D:S.338, D:S.338 Salt bridges: D:K.209, D:R.373 SO4.17: 2 residues within 4Å: Chain D: E.177, G.178 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.178 Water bridges: D:V.179, D:V.179, D:V.179 SO4.18: 5 residues within 4Å: Chain D: E.276, K.279, F.292, E.293, D.294 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.293, D:D.294 Salt bridges: D:K.279

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 12 residues within 4Å: Chain A: T.57, R.58, L.59, G.60, V.64, E.68, A.82, T.83, R.233, S.243, V.244, I.245 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.57, A:L.59, A:R.233, A:S.243, A:I.245 Water bridges: A:N.61 GOL.14: 12 residues within 4Å: Chain C: T.57, R.58, L.59, G.60, V.64, E.68, A.82, T.83, R.233, S.243, V.244, I.245 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.57, C:L.59, C:R.233, C:S.243, C:I.245 Water bridges: C:N.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goodall, G. et al., The Structure and Proposed Catalytic Mechanism of Methionine Gamma-Lyase. To be Published

Release Date

2001-07-19

Peptides

METHIONINE GAMMA-LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

METHIONINE GAMMA-LYASE

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