SMTL ID : 1kyv.1 (1 other biounit)

Lumazine Synthase from S.pombe bound to riboflavin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-pentamer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: G.90, S.91, T.92 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:G.90, 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: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.90, B:S.91, B:T.92 Water bridges: B:G.90, B:G.90 Salt bridges: A:R.133 PO4.5: 6 residues within 4Å: Chain B: R.133 Chain C: G.90, S.91, T.92, H.94 Ligands: RBF.6 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.91, C:T.92, C:T.92 Water bridges: C:G.90, C:G.90, 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 Water bridges: D:G.90 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 Water bridges: E:G.90, E:G.90 Salt bridges: D:R.133

5 x RBF: RIBOFLAVIN(Non-covalent)

RBF.2: 15 residues within 4Å: Chain A: W.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, I.98 Chain E: I.118, L.119, H.142, W.146 Ligands: PO4.1 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:W.27, E:W.146 Hydrogen bonds: A:S.62, A:W.63, A:V.86, A:I.88, E:L.119 Water bridges: A:V.86 pi-Stacking: A:W.27, A:W.27, A:W.27, A:H.94 RBF.4: 14 residues within 4Å: Chain A: I.118, L.119, H.142, W.146 Chain B: W.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.3 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.27, B:W.27, A:W.146 Hydrogen bonds: B:S.62, B:W.63, B:W.63, B:E.64, B:V.86, B:I.88, A:L.119 Water bridges: B:V.86 pi-Stacking: B:W.27, B:W.27, B:W.27, B:H.94 RBF.6: 15 residues within 4Å: Chain B: I.118, L.119, H.142, W.146 Chain C: W.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, I.98 Ligands: PO4.5 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.27, B:W.146 Hydrogen bonds: C:S.62, C:W.63, C:E.64, C:V.86, C:I.88, B:L.119 Water bridges: C:V.86 pi-Stacking: C:W.27, C:W.27, C:W.27, C:H.94 RBF.8: 15 residues within 4Å: Chain C: I.118, L.119, H.142, W.146 Chain D: W.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, I.98 Ligands: PO4.7 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.27, D:W.27, C:W.146 Hydrogen bonds: D:S.62, D:W.63, D:E.64, D:V.86, D:I.88, C:L.119 Water bridges: D:V.86 pi-Stacking: D:W.27, D:W.27, D:W.27, D:H.94 RBF.10: 15 residues within 4Å: Chain D: I.118, L.119, H.142, W.146 Chain E: W.27, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, I.98 Ligands: PO4.9 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:W.27, E:W.27, D:W.146 Hydrogen bonds: E:S.62, E:W.63, E:E.64, E:V.86, E:I.88, D:L.119 Water bridges: E:V.86 pi-Stacking: E:W.27, E:W.27, E:W.27, E:H.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gerhardt, S. et al., The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase. J.Mol.Biol. (2002)

Release Date

2002-07-24

Peptides

6,7-Dimethyl-8-ribityllumazine Synthase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

6,7-Dimethyl-8-ribityllumazine Synthase

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