SMTL ID : 4oma.1

The crystal structure of methionine gamma-lyase from Citrobacter freundii in complex with L-cycloserine pyridoxal-5'-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x LCS: [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

LCS.1: 20 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, I.219, G.220, V.338, S.339, L.340, R.374 Chain C: Y.58, R.60 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.113 Hydrogen bonds: A:G.88, A:I.89, A:T.187, A:T.209, A:K.210, A:G.220, A:S.339, A:R.374, A:R.374, C:Y.58 Salt bridges: A:K.210, C:R.60 pi-Cation interactions: A:K.210 LCS.7: 20 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, I.219, G.220, V.338, S.339, L.340, R.374 Chain D: Y.58, R.60 14 PLIP interactions: 2 interactions with chain D, 12 interactions with chain B Hydrogen bonds: D:Y.58, B:G.88, B:I.89, B:T.187, B:T.209, B:K.210, B:G.220, B:S.339, B:R.374, B:R.374 Salt bridges: D:R.60, B:K.210 Hydrophobic interactions: B:Y.113 pi-Cation interactions: B:K.210 LCS.13: 20 residues within 4Å: Chain A: Y.58, R.60 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, I.219, G.220, V.338, S.339, L.340, R.374 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.113 Hydrogen bonds: C:G.88, C:I.89, C:Y.113, C:K.210, C:G.220, C:S.339, C:R.374, C:R.374 Water bridges: C:E.156 Salt bridges: C:K.210, A:R.60 pi-Cation interactions: C:K.210 LCS.19: 20 residues within 4Å: Chain B: Y.58, R.60 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, I.219, G.220, V.338, S.339, L.340, R.374 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain D Salt bridges: B:R.60, D:K.210 Hydrophobic interactions: D:Y.113 Hydrogen bonds: D:G.88, D:I.89, D:Y.113, D:K.210, D:G.220, D:S.339, D:R.374, D:R.374 Water bridges: D:E.156 pi-Cation interactions: D:K.210

8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 10 residues within 4Å: Chain A: P.191, Y.192, C.193, Q.195, Q.303, R.304, Q.305, M.306, S.307 Ligands: PEG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.192, A:Q.303, A:S.307 PGE.3: 4 residues within 4Å: Chain A: E.270, K.274, P.382, E.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.274, A:E.383 PGE.8: 10 residues within 4Å: Chain B: P.191, Y.192, C.193, Q.195, Q.303, R.304, Q.305, M.306, S.307 Ligands: PEG.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.192, B:Q.303, B:S.307 PGE.9: 4 residues within 4Å: Chain B: E.270, K.274, P.382, E.383 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.274, B:E.383 PGE.14: 10 residues within 4Å: Chain C: P.191, Y.192, C.193, Q.195, Q.303, R.304, Q.305, M.306, S.307 Ligands: PEG.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.192, C:Q.303, C:S.307 PGE.15: 4 residues within 4Å: Chain C: E.270, K.274, P.382, E.383 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.274, C:E.383, C:E.383 Water bridges: C:E.270 PGE.20: 10 residues within 4Å: Chain D: P.191, Y.192, C.193, Q.195, Q.303, R.304, Q.305, M.306, S.307 Ligands: PEG.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.192, D:Q.303, D:S.307 PGE.21: 4 residues within 4Å: Chain D: E.270, K.274, P.382, E.383 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.274, D:E.383, D:E.383 Water bridges: D:E.270

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

PEG.4: 7 residues within 4Å: Chain A: L.273, R.277, E.280, G.292, L.293, S.294, S.295 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.277, A:E.280, A:S.294, A:S.295 Water bridges: A:G.292 PEG.5: 5 residues within 4Å: Chain A: F.9, Y.192, E.266, S.307 Ligands: PGE.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.307 Water bridges: A:F.9, A:N.10, A:Y.192, A:Y.192, A:E.266 PEG.10: 7 residues within 4Å: Chain B: L.273, R.277, E.280, G.292, L.293, S.294, S.295 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.277, B:E.280, B:S.294, B:S.295 Water bridges: B:G.292 PEG.11: 5 residues within 4Å: Chain B: F.9, Y.192, E.266, S.307 Ligands: PGE.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.307 Water bridges: B:F.9, B:N.10, B:Y.192, B:Y.192, B:E.266 PEG.16: 7 residues within 4Å: Chain C: L.273, R.277, E.280, G.292, L.293, S.294, S.295 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.277, C:E.280, C:S.294, C:S.295 Water bridges: C:G.292 PEG.17: 5 residues within 4Å: Chain C: F.9, Y.192, E.266, S.307 Ligands: PGE.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.307 Water bridges: C:F.9, C:N.10, C:N.10, C:Y.192, C:Y.192 PEG.22: 7 residues within 4Å: Chain D: L.273, R.277, E.280, G.292, L.293, S.294, S.295 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.277, D:E.280, D:S.294, D:S.295 Water bridges: D:G.292 PEG.23: 5 residues within 4Å: Chain D: F.9, Y.192, E.266, S.307 Ligands: PGE.20 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.307 Water bridges: D:F.9, D:N.10, D:N.10, D:Y.192, D:Y.192

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 7 residues within 4Å: Chain A: N.271, I.275, V.377, G.378, E.380, P.382, I.385 Ligand excluded by PLIP CL.12: 7 residues within 4Å: Chain B: N.271, I.275, V.377, G.378, E.380, P.382, I.385 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain C: N.271, I.275, V.377, G.378, E.380, P.382, I.385 Ligand excluded by PLIP CL.24: 7 residues within 4Å: Chain D: N.271, I.275, V.377, G.378, E.380, P.382, I.385 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuznetsov, N.A. et al., Pre-steady-state Kinetic and Structural Analysis of Interaction of Methionine gamma-Lyase from Citrobacter freundii with Inhibitors. J.Biol.Chem. (2015)

Release Date

2014-11-26

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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