SMTL ID : 3jwb.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-tetramer

Ligands

4 x NLE: NORLEUCINE(Non-covalent)

NLE.1: 8 residues within 4Å: Chain A: Y.113, C.115, K.210, V.338, S.339, L.340, R.374 Chain C: Y.58 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.113, A:V.338, C:Y.58 Hydrogen bonds: A:S.339, C:Y.58 Water bridges: A:R.374 Salt bridges: A:R.374 NLE.5: 8 residues within 4Å: Chain B: Y.113, C.115, K.210, V.338, S.339, L.340, R.374 Chain D: Y.58 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Y.113, B:V.338, D:Y.58 Hydrogen bonds: B:S.339, D:Y.58 Water bridges: B:R.374 Salt bridges: B:R.374 NLE.9: 8 residues within 4Å: Chain A: Y.58 Chain C: Y.113, C.115, K.210, V.338, S.339, L.340, R.374 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:Y.58, C:Y.113, C:V.338 Hydrogen bonds: A:Y.58, C:Y.113, C:S.339 Water bridges: C:R.374 Salt bridges: C:R.374 NLE.13: 8 residues within 4Å: Chain B: Y.58 Chain D: Y.113, C.115, K.210, V.338, S.339, L.340, R.374 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.113, D:V.338, B:Y.58 Hydrogen bonds: D:Y.113, D:S.339, B:Y.58 Water bridges: D:R.374 Salt bridges: D:R.374

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

PEG.2: 6 residues within 4Å: Chain A: P.191, Y.192, C.193, M.306, S.307 Ligands: PEG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.191, A:S.307 Water bridges: A:Q.303, A:M.306 PEG.3: 6 residues within 4Å: Chain A: F.9, Y.192, E.266, S.307, L.308 Ligands: PEG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.307 PEG.4: 2 residues within 4Å: Chain A: E.270, K.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.274 PEG.6: 6 residues within 4Å: Chain B: P.191, Y.192, C.193, M.306, S.307 Ligands: PEG.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.191, B:S.307 Water bridges: B:Q.303, B:M.306 PEG.7: 6 residues within 4Å: Chain B: F.9, Y.192, E.266, S.307, L.308 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.307 PEG.8: 2 residues within 4Å: Chain B: E.270, K.274 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.274 PEG.10: 6 residues within 4Å: Chain C: P.191, Y.192, C.193, M.306, S.307 Ligands: PEG.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.191, C:S.307 Water bridges: C:Q.303, C:M.306 PEG.11: 6 residues within 4Å: Chain C: F.9, Y.192, E.266, S.307, L.308 Ligands: PEG.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.307 PEG.12: 2 residues within 4Å: Chain C: E.270, K.274 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.274 PEG.14: 6 residues within 4Å: Chain D: P.191, Y.192, C.193, M.306, S.307 Ligands: PEG.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:P.191, D:S.307 Water bridges: D:Q.303, D:M.306 PEG.15: 6 residues within 4Å: Chain D: F.9, Y.192, E.266, S.307, L.308 Ligands: PEG.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.307 PEG.16: 2 residues within 4Å: Chain D: E.270, K.274 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.274

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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