SMTL ID : 6lxu.1

Crystal structure of methionine gamma-lyase from Fusobacterium nucleatum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

homo-tetramer

Ligands

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 9 residues within 4Å: Chain A: Y.114, C.116, V.340, S.341 Chain C: F.50, Y.59, R.61, L.62 Ligands: NO3.2 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:V.340, C:F.50, C:Y.59, C:L.62 Water bridges: A:Y.114 MPD.4: 9 residues within 4Å: Chain B: Y.114, C.116, V.340, S.341 Chain D: F.50, Y.59, R.61, L.62 Ligands: NO3.5 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.50, D:Y.59, D:L.62, B:V.340 Water bridges: B:Y.114 MPD.7: 9 residues within 4Å: Chain A: F.50, Y.59, R.61, L.62 Chain C: Y.114, C.116, V.340, S.341 Ligands: NO3.8 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.340, A:F.50, A:Y.59, A:L.62 Hydrogen bonds: C:Y.114 Water bridges: C:Y.114 MPD.10: 9 residues within 4Å: Chain B: F.50, Y.59, R.61, L.62 Chain D: Y.114, C.116, V.340, S.341 Ligands: NO3.11 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:F.50, B:Y.59, B:L.62, D:V.340 Hydrogen bonds: D:Y.114 Water bridges: D:Y.114

8 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 7 residues within 4Å: Chain A: Y.114, V.340, S.341, L.342, Q.350, R.376 Ligands: MPD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.341, A:Q.350, A:R.376, A:R.376 Water bridges: A:N.161 NO3.3: 3 residues within 4Å: Chain A: G.56, L.62, G.63 2 PLIP interactions: 2 interactions with chain A Water bridges: A:I.58, A:G.63 NO3.5: 7 residues within 4Å: Chain B: Y.114, V.340, S.341, L.342, Q.350, R.376 Ligands: MPD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.341, B:Q.350, B:R.376, B:R.376 Water bridges: B:N.161 NO3.6: 3 residues within 4Å: Chain B: G.56, L.62, G.63 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.58, B:G.63 NO3.8: 7 residues within 4Å: Chain C: Y.114, V.340, S.341, L.342, Q.350, R.376 Ligands: MPD.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.341, C:Q.350, C:R.376, C:R.376 Water bridges: C:N.161 NO3.9: 3 residues within 4Å: Chain C: G.56, L.62, G.63 2 PLIP interactions: 2 interactions with chain C Water bridges: C:I.58, C:G.63 NO3.11: 7 residues within 4Å: Chain D: Y.114, V.340, S.341, L.342, Q.350, R.376 Ligands: MPD.10 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.341, D:Q.350, D:R.376, D:R.376 Water bridges: D:N.161 NO3.12: 3 residues within 4Å: Chain D: G.56, L.62, G.63 2 PLIP interactions: 2 interactions with chain D Water bridges: D:I.58, D:G.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kezuka, Y., Crystal structure of methionine gamma-lyase from Fusobacterium nucleatum. To Be Published

Release Date

2021-02-17

Peptides

L-methionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

L-methionine gamma-lyase