SMTL ID : 4hf8.1

Crystal structure of L-methionine gamma-lyase from Citrobacter freundii with glycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

4 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

PLG.1: 20 residues within 4Å: Chain A: S.87, G.88, I.89, I.92, Y.113, E.156, N.160, D.185, T.187, F.188, S.207, T.209, K.210, G.220, V.338, S.339, L.340, R.374 Chain C: Y.58, R.60 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.113, A:E.156 Hydrogen bonds: A:G.88, A:I.89, A:N.160, A:N.160, A:T.187, A:S.207, A:T.209, A:T.209, A:K.210, A:S.339, C:Y.58 Water bridges: A:R.374, A:R.374 Salt bridges: A:K.210, A:K.210, A:R.374, C:R.60 PLG.6: 20 residues within 4Å: Chain B: S.87, G.88, I.89, I.92, Y.113, E.156, N.160, D.185, T.187, F.188, S.207, T.209, K.210, G.220, V.338, S.339, L.340, R.374 Chain D: Y.58, R.60 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Y.113, B:E.156 Hydrogen bonds: B:G.88, B:I.89, B:N.160, B:N.160, B:T.187, B:S.207, B:T.209, B:T.209, B:K.210, B:S.339, D:Y.58 Water bridges: B:R.374, B:R.374 Salt bridges: B:K.210, B:K.210, B:R.374, D:R.60 PLG.11: 20 residues within 4Å: Chain A: Y.58, R.60 Chain C: S.87, G.88, I.89, I.92, Y.113, E.156, N.160, D.185, T.187, F.188, S.207, T.209, K.210, G.220, V.338, S.339, L.340, R.374 17 PLIP interactions: 1 interactions with chain A, 16 interactions with chain C Salt bridges: A:R.60, C:K.210, C:K.210, C:R.374 Hydrophobic interactions: C:Y.113, C:E.156 Hydrogen bonds: C:G.88, C:I.89, C:N.160, C:N.160, C:S.207, C:T.209, C:K.210, C:S.339 Water bridges: C:Y.154, C:R.374, C:R.374 PLG.16: 20 residues within 4Å: Chain B: Y.58, R.60 Chain D: S.87, G.88, I.89, I.92, Y.113, E.156, N.160, D.185, T.187, F.188, S.207, T.209, K.210, G.220, V.338, S.339, L.340, R.374 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.113, D:E.156 Hydrogen bonds: D:G.88, D:I.89, D:N.160, D:N.160, D:S.207, D:T.209, D:K.210, D:S.339 Water bridges: D:Y.154, D:R.374, D:R.374 Salt bridges: D:K.210, D:K.210, D:R.374, B:R.60

4 x GLY: GLYCINE(Non-covalent)

GLY.2: 2 residues within 4Å: Chain A: H.355, V.358 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A Water bridges: G.2, G.2 Hydrogen bonds: A:H.355 Salt bridges: A:H.355 GLY.7: 2 residues within 4Å: Chain B: H.355, V.358 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain B Water bridges: G.7, G.7 Hydrogen bonds: B:H.355 Salt bridges: B:H.355 GLY.12: 2 residues within 4Å: Chain C: H.355, V.358 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:H.355 Salt bridges: C:H.355 Water bridges: G.12, G.12 GLY.17: 2 residues within 4Å: Chain D: H.355, V.358 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain D Water bridges: G.17, G.17 Hydrogen bonds: D:H.355 Salt bridges: D:H.355

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

PEG.3: 9 residues within 4Å: Chain A: P.191, Y.192, C.193, Q.194, Q.195, R.304, Q.305, M.306, S.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.192, A:S.307, A:S.307 Water bridges: A:Q.195 PEG.4: 8 residues within 4Å: Chain A: Q.18, S.28, W.252, L.255, R.256, K.259 Chain B: H.215, D.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.18 Water bridges: A:T.29 PEG.5: 9 residues within 4Å: Chain A: R.267, N.271, K.274, L.379, E.380, D.381, P.382, E.383 Chain B: N.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.267, A:N.271, A:K.274, A:L.379, A:D.381, A:E.383 PEG.8: 9 residues within 4Å: Chain B: P.191, Y.192, C.193, Q.194, Q.195, R.304, Q.305, M.306, S.307 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.192, B:S.307, B:S.307 Water bridges: B:Q.195 PEG.9: 8 residues within 4Å: Chain A: H.215, D.217 Chain B: Q.18, S.28, W.252, L.255, R.256, K.259 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.18 Water bridges: B:T.29 PEG.10: 9 residues within 4Å: Chain A: N.10 Chain B: R.267, N.271, K.274, L.379, E.380, D.381, P.382, E.383 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.267, B:N.271, B:K.274, B:L.379, B:D.381, B:E.383 PEG.13: 9 residues within 4Å: Chain C: P.191, Y.192, C.193, Q.194, Q.195, R.304, Q.305, M.306, S.307 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.192, C:S.307, C:S.307 Water bridges: C:Q.195 PEG.14: 8 residues within 4Å: Chain C: Q.18, S.28, W.252, L.255, R.256, K.259 Chain D: H.215, D.217 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.217, C:Q.18 Water bridges: C:T.29, C:T.29 PEG.15: 9 residues within 4Å: Chain C: R.267, N.271, K.274, L.379, E.380, D.381, P.382, E.383 Chain D: N.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.267, C:N.271, C:K.274, C:L.379, C:E.383 PEG.18: 9 residues within 4Å: Chain D: P.191, Y.192, C.193, Q.194, Q.195, R.304, Q.305, M.306, S.307 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.192, D:S.307, D:S.307 Water bridges: D:Q.195 PEG.19: 8 residues within 4Å: Chain C: H.215, D.217 Chain D: Q.18, S.28, W.252, L.255, R.256, K.259 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.18, C:D.217 Water bridges: D:T.29, D:T.29 PEG.20: 9 residues within 4Å: Chain C: N.10 Chain D: R.267, N.271, K.274, L.379, E.380, D.381, P.382, E.383 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.267, D:N.271, D:K.274, D:L.379, D:E.383

Links

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Citation

Revtovich, S.V. et al., Crystal structure of the external aldimine of Citrobacter freundii methionine gamma-lyase with glycine provides insight in mechanisms of two stages of physiological reaction and isotope exchange of alpha- and beta-protons of competitive inhibitors. Biochimie (2014)

Release Date

2013-11-06

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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