SMTL ID : 3jwa.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

4 x MPJ: (1-AMINO-3-METHYLSULFANYL-PROPYL)-PHOSPHINIC ACID(Non-covalent)

MPJ.1: 10 residues within 4Å: Chain A: Y.113, C.115, K.210, V.338, S.339, L.340, Q.348, R.374 Chain C: Y.58, L.61 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.338 Hydrogen bonds: A:Y.113, A:S.339, A:R.374, A:R.374 MPJ.7: 10 residues within 4Å: Chain B: Y.113, C.115, K.210, V.338, S.339, L.340, Q.348, R.374 Chain D: Y.58, L.61 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.338 Hydrogen bonds: B:Y.113, B:S.339, B:R.374, B:R.374 MPJ.13: 10 residues within 4Å: Chain A: Y.58, L.61 Chain C: Y.113, C.115, K.210, V.338, S.339, L.340, Q.348, R.374 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.338 Hydrogen bonds: C:Y.113, C:Y.113, C:S.339, C:R.374, C:R.374 MPJ.19: 10 residues within 4Å: Chain B: Y.58, L.61 Chain D: Y.113, C.115, K.210, V.338, S.339, L.340, Q.348, R.374 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.338 Hydrogen bonds: D:Y.113, D:Y.113, D:S.339, D:R.374, D:R.374

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

PEG.2: 6 residues within 4Å: Chain A: P.191, Y.192, Q.195, Q.305, M.306, S.307 Ligand excluded by PLIP PEG.3: 4 residues within 4Å: Chain A: E.270, K.274, P.382, E.383 Ligand excluded by PLIP PEG.4: 5 residues within 4Å: Chain A: F.9, Y.192, E.266, S.307, L.308 Ligand excluded by PLIP PEG.5: 7 residues within 4Å: Chain A: P.291, G.302, Q.303, M.306, S.307, L.308, P.309 Ligand excluded by PLIP PEG.6: 8 residues within 4Å: Chain A: G.103, D.104, H.105, N.130, V.131, S.132, R.147, E.149 Ligand excluded by PLIP PEG.8: 6 residues within 4Å: Chain B: P.191, Y.192, Q.195, Q.305, M.306, S.307 Ligand excluded by PLIP PEG.9: 4 residues within 4Å: Chain B: E.270, K.274, P.382, E.383 Ligand excluded by PLIP PEG.10: 5 residues within 4Å: Chain B: F.9, Y.192, E.266, S.307, L.308 Ligand excluded by PLIP PEG.11: 7 residues within 4Å: Chain B: P.291, G.302, Q.303, M.306, S.307, L.308, P.309 Ligand excluded by PLIP PEG.12: 8 residues within 4Å: Chain B: G.103, D.104, H.105, N.130, V.131, S.132, R.147, E.149 Ligand excluded by PLIP PEG.14: 6 residues within 4Å: Chain C: P.191, Y.192, Q.195, Q.305, M.306, S.307 Ligand excluded by PLIP PEG.15: 4 residues within 4Å: Chain C: E.270, K.274, P.382, E.383 Ligand excluded by PLIP PEG.16: 5 residues within 4Å: Chain C: F.9, Y.192, E.266, S.307, L.308 Ligand excluded by PLIP PEG.17: 7 residues within 4Å: Chain C: P.291, G.302, Q.303, M.306, S.307, L.308, P.309 Ligand excluded by PLIP PEG.18: 8 residues within 4Å: Chain C: G.103, D.104, H.105, N.130, V.131, S.132, R.147, E.149 Ligand excluded by PLIP PEG.20: 6 residues within 4Å: Chain D: P.191, Y.192, Q.195, Q.305, M.306, S.307 Ligand excluded by PLIP PEG.21: 4 residues within 4Å: Chain D: E.270, K.274, P.382, E.383 Ligand excluded by PLIP PEG.22: 5 residues within 4Å: Chain D: F.9, Y.192, E.266, S.307, L.308 Ligand excluded by PLIP PEG.23: 7 residues within 4Å: Chain D: P.291, G.302, Q.303, M.306, S.307, L.308, P.309 Ligand excluded by PLIP PEG.24: 8 residues within 4Å: Chain D: G.103, D.104, H.105, N.130, V.131, S.132, R.147, E.149 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Revtovich, S.V. et al., Three-dimensional structures of noncovalent complexes of Citrobacter freundii methionine gamma-lyase with substrates. Biochemistry Mosc. (2011)

Release Date

2010-09-08

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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