SMTL ID : 2a58.2 (1 other biounit)

Structure of 6,7-Dimethyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound riboflavin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-10-mer

Ligands

10 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: G.90, S.91, T.92, H.94 Chain E: R.133 Ligands: RBF.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:S.91, A:T.92, A:T.92, A:T.92 Water bridges: A:T.92, A:F.95 Salt bridges: E:R.133 PO4.3: 6 residues within 4Å: Chain A: R.133 Chain B: G.90, S.91, T.92, H.94 Ligands: RBF.4 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Salt bridges: A:R.133 Hydrogen bonds: B:S.91, B:T.92, B:T.92 Water bridges: B:G.90, B:T.92 PO4.5: 6 residues within 4Å: Chain B: R.133 Chain C: G.90, S.91, T.92, H.94 Ligands: RBF.6 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.91, C:T.92, C:T.92 Water bridges: C:T.92, C:T.92, C:F.95, B:R.133 Salt bridges: B:R.133 PO4.7: 6 residues within 4Å: Chain C: R.133 Chain D: G.90, S.91, T.92, H.94 Ligands: RBF.8 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.91, D:T.92, D:T.92 Salt bridges: C:R.133 PO4.9: 6 residues within 4Å: Chain D: R.133 Chain E: G.90, S.91, T.92, H.94 Ligands: RBF.10 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.91, E:T.92, E:T.92 Water bridges: E:F.95 Salt bridges: D:R.133 PO4.11: 6 residues within 4Å: Chain F: G.90, S.91, T.92, H.94 Chain J: R.133 Ligands: RBF.12 7 PLIP interactions: 1 interactions with chain J, 6 interactions with chain F Salt bridges: J:R.133 Hydrogen bonds: F:S.91, F:T.92, F:T.92, F:T.92 Water bridges: F:T.92, F:F.95 PO4.13: 6 residues within 4Å: Chain F: R.133 Chain G: G.90, S.91, T.92, H.94 Ligands: RBF.14 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:S.91, G:T.92, G:T.92 Water bridges: G:G.90 Salt bridges: F:R.133 PO4.15: 6 residues within 4Å: Chain G: R.133 Chain H: G.90, S.91, T.92, H.94 Ligands: RBF.16 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:S.91, H:T.92, H:T.92 Water bridges: H:T.92, H:H.94, H:F.95 Salt bridges: G:R.133 PO4.17: 6 residues within 4Å: Chain H: R.133 Chain I: G.90, S.91, T.92, H.94 Ligands: RBF.18 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain I Salt bridges: H:R.133 Hydrogen bonds: I:S.91, I:T.92, I:T.92 PO4.19: 6 residues within 4Å: Chain I: R.133 Chain J: G.90, S.91, T.92, H.94 Ligands: RBF.20 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:S.91, J:T.92, J:T.92 Water bridges: J:T.92, J:F.95 Salt bridges: I:R.133

10 x RBF: RIBOFLAVIN(Non-covalent)

RBF.2: 15 residues within 4Å: Chain A: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Chain E: I.118, L.119, H.142, W.146, A.149 Ligands: PO4.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.62, A:W.63, A:E.64, A:V.86, A:I.88 Water bridges: A:V.86 pi-Cation interactions: A:H.94 RBF.4: 15 residues within 4Å: Chain A: I.118, L.119, H.142, W.146, A.149 Chain B: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.62, B:W.63, B:E.64, B:V.86, B:I.88 pi-Cation interactions: B:H.94 RBF.6: 15 residues within 4Å: Chain B: I.118, L.119, H.142, W.146, A.149 Chain C: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.5 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.62, C:W.63, C:E.64, C:V.86, C:I.88 Water bridges: C:V.86 pi-Cation interactions: C:H.94 RBF.8: 15 residues within 4Å: Chain C: I.118, L.119, H.142, W.146, A.149 Chain D: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.62, D:W.63, D:E.64, D:V.86, D:I.88 pi-Cation interactions: D:H.94 RBF.10: 15 residues within 4Å: Chain D: I.118, L.119, H.142, W.146, A.149 Chain E: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.9 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain E Water bridges: D:L.119, D:L.121 Hydrogen bonds: E:S.62, E:W.63, E:E.64, E:V.86, E:I.88 pi-Cation interactions: E:H.94 RBF.12: 15 residues within 4Å: Chain F: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Chain J: I.118, L.119, H.142, W.146, A.149 Ligands: PO4.11 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.62, F:W.63, F:E.64, F:V.86, F:I.88 Water bridges: F:V.86 pi-Cation interactions: F:H.94 RBF.14: 15 residues within 4Å: Chain F: I.118, L.119, H.142, W.146, A.149 Chain G: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.13 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:S.62, G:W.63, G:E.64, G:V.86, G:I.88 pi-Cation interactions: G:H.94 RBF.16: 15 residues within 4Å: Chain G: I.118, L.119, H.142, W.146, A.149 Chain H: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.15 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:S.62, H:W.63, H:E.64, H:V.86, H:I.88 Water bridges: H:V.86 pi-Cation interactions: H:H.94 RBF.18: 15 residues within 4Å: Chain H: I.118, L.119, H.142, W.146, A.149 Chain I: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.17 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:S.62, I:W.63, I:E.64, I:V.86, I:I.88 pi-Cation interactions: I:H.94 RBF.20: 15 residues within 4Å: Chain I: I.118, L.119, H.142, W.146, A.149 Chain J: Y.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.19 8 PLIP interactions: 6 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:S.62, J:W.63, J:E.64, J:V.86, J:I.88 pi-Cation interactions: J:H.94 Water bridges: I:L.119, I:L.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koch, M. et al., Structural basis of charge transfer complex formation by riboflavin bound to 6,7-dimethyl-8-ribityllumazine synthase. Eur.J.Biochem. (2004)

Release Date

2005-07-19

Peptides

6,7-dimethyl-8-ribityllumazine synthase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

6,7-dimethyl-8-ribityllumazine synthase

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