SMTL ID : 2a59.1

Structure of 6,7-Dimethyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 5-nitroso-6-ribitylamino-2,4(1H,3H)-pyrimidinedione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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, H.94 Chain E: R.133 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain A Salt bridges: E:R.133 Hydrogen bonds: A:S.91, A:T.92, A:T.92, A:T.92 Water bridges: A:F.95 PO4.3: 5 residues within 4Å: Chain A: R.133 Chain B: G.90, S.91, T.92, H.94 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.91, B:T.92, B:T.92 Water bridges: B:T.92, B:H.94, B:F.95, A:R.133 Salt bridges: A:R.133 PO4.5: 5 residues within 4Å: Chain B: R.133 Chain C: G.90, S.91, T.92, H.94 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:H.94, B:R.133 Salt bridges: B:R.133 PO4.7: 5 residues within 4Å: Chain C: R.133 Chain D: G.90, S.91, T.92, H.94 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Water bridges: C:R.133, D:G.90, D:T.92, D:H.94 Salt bridges: C:R.133 Hydrogen bonds: D:S.91, D:T.92, D:T.92 PO4.9: 5 residues within 4Å: Chain D: R.133 Chain E: G.90, S.91, T.92, H.94 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.91, E:T.92, E:T.92 Water bridges: E:G.90, E:T.92, E:T.92 Salt bridges: D:R.133

5 x LMZ: 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE(Non-covalent)

LMZ.2: 13 residues within 4Å: Chain A: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Chain E: I.118, L.119, W.146 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:N.28, A:S.62, A:W.63, A:V.86, A:I.88, E:L.119 Water bridges: A:Y.27, A:V.86 pi-Stacking: A:Y.27 LMZ.4: 13 residues within 4Å: Chain A: I.118, L.119, W.146 Chain B: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.28, B:S.62, B:W.63, B:V.86, B:I.88, A:L.119 Water bridges: B:V.86 pi-Stacking: B:Y.27 LMZ.6: 13 residues within 4Å: Chain B: I.118, L.119, W.146 Chain C: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.28, C:S.62, C:W.63, C:V.86, C:I.88, B:L.119 Water bridges: C:V.86 pi-Stacking: C:Y.27 LMZ.8: 13 residues within 4Å: Chain C: I.118, L.119, W.146 Chain D: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:L.119, D:N.28, D:S.62, D:W.63, D:V.86, D:I.88 Water bridges: D:Y.27 pi-Stacking: D:Y.27 LMZ.10: 13 residues within 4Å: Chain D: I.118, L.119, W.146 Chain E: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:N.28, E:S.62, E:W.63, E:V.86, E:I.88, D:L.119 Water bridges: E:Y.27 pi-Stacking: E:Y.27

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: 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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