SMTL ID : 1e5e.1

METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS IN COMPLEX WITH PROPARGYLGLYCINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-tetramer

Ligands

4 x PPJ: N-(HYDROXY{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)NORVALINE(Covalent)

PPJ.1: 21 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, V.337, S.338, L.339, T.353, R.373 Chain B: Y.56, R.58 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.111, A:Y.111, A:V.337, A:T.353, B:Y.56 Hydrogen bonds: A:S.85, A:G.86, A:M.87, A:N.158, A:S.206, A:S.206, A:K.209, A:S.338, B:Y.56 Water bridges: A:T.114 Salt bridges: A:K.209, A:K.209, A:R.373, B:R.58 PPJ.5: 21 residues within 4Å: Chain A: Y.56, R.58 Chain B: S.85, G.86, M.87, I.90, Y.111, N.158, D.184, T.186, F.187, S.206, T.208, K.209, V.218, A.219, V.337, S.338, L.339, T.353, R.373 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.111, B:Y.111, B:V.337, B:T.353, A:Y.56 Hydrogen bonds: B:S.85, B:G.86, B:M.87, B:N.158, B:S.206, B:T.208, B:S.338, A:Y.56 Salt bridges: B:K.209, B:K.209, B:R.373, A:R.58 PPJ.10: 21 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, V.337, S.338, L.339, T.353, R.373 Chain D: Y.56, R.58 20 PLIP interactions: 2 interactions with chain D, 18 interactions with chain C Hydrophobic interactions: D:Y.56, C:Y.111, C:Y.111, C:V.337, C:T.353 Salt bridges: D:R.58, C:K.209, C:K.209, C:R.373 Hydrogen bonds: C:S.85, C:G.86, C:M.87, C:N.158, C:T.186, C:S.206, C:S.206, C:T.208, C:K.209, C:S.338 Water bridges: C:D.184 PPJ.14: 21 residues within 4Å: Chain C: Y.56, R.58 Chain D: S.85, G.86, M.87, I.90, Y.111, N.158, D.184, T.186, F.187, S.206, T.208, K.209, V.218, A.219, V.337, S.338, L.339, T.353, R.373 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.111, D:Y.111, D:V.337, D:T.353, C:Y.56 Hydrogen bonds: D:S.85, D:G.86, D:M.87, D:N.158, D:T.186, D:S.206, D:S.338 Water bridges: D:D.184 Salt bridges: D:K.209, D:K.209, D:R.373, C:R.58

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

SO4.2: 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 SO4.3: 3 residues within 4Å: Chain A: K.279, K.286, D.294 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.287 Salt bridges: A:K.279, A:K.286 SO4.6: 3 residues within 4Å: Chain B: P.358, K.359, R.362 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.359 Water bridges: B:A.355, B:V.357, B:R.362, B:R.362 Salt bridges: B:R.362 SO4.7: 4 residues within 4Å: Chain B: K.279, F.292, E.293, D.294 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.293, B:D.294 Salt bridges: B:K.279 SO4.8: 3 residues within 4Å: Chain B: P.282, V.284, K.317 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.284 Salt bridges: B:K.317 SO4.11: 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 SO4.12: 3 residues within 4Å: Chain C: K.279, K.286, D.294 3 PLIP interactions: 3 interactions with chain C Water bridges: C:V.287 Salt bridges: C:K.279, C:K.286 SO4.15: 3 residues within 4Å: Chain D: P.358, K.359, R.362 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.359 Water bridges: D:A.355, D:V.357, D:R.362, D:R.362 Salt bridges: D:R.362 SO4.16: 4 residues within 4Å: Chain D: 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 SO4.17: 3 residues within 4Å: Chain D: P.282, V.284, K.317 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.284 Salt bridges: D:K.317

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 12 residues within 4Å: Chain A: T.57, R.58, L.59, G.60, V.64, A.82, T.83, R.233, I.237, S.243, V.244, I.245 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.59, A:R.233, A:S.243, A:I.245 Water bridges: A:T.57 GOL.9: 3 residues within 4Å: Chain B: E.293, H.298, K.302 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.298 GOL.13: 12 residues within 4Å: Chain C: T.57, R.58, L.59, G.60, V.64, A.82, T.83, R.233, I.237, S.243, V.244, I.245 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.59, C:R.233, C:S.243, C:I.245 Water bridges: C:T.57 GOL.18: 3 residues within 4Å: Chain D: E.293, H.298, K.302 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.298

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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