SMTL ID : 2a57.2 (1 other biounit)

Structure of 6,7-Dimthyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 6-carboxyethyl-7-oxo-8-ribityllumazine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-10-mer

Ligands

10 x CRM: 3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID(Non-covalent)

CRM.1: 14 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 Ligands: PO4.9 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:S.62, A:W.63, A:E.64, A:V.86, A:I.88, E:L.119 pi-Stacking: A:Y.27, A:Y.27 CRM.4: 14 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 Ligands: PO4.2 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.62, B:W.63, B:E.64, B:V.86, B:I.88, A:L.119 pi-Stacking: B:Y.27, B:Y.27 CRM.5: 14 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 Ligands: PO4.3 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.62, C:W.63, C:E.64, C:V.86, C:I.88, B:L.119 pi-Stacking: C:Y.27, C:Y.27 CRM.7: 14 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 Ligands: PO4.6 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.62, D:W.63, D:E.64, D:V.86, D:I.88, C:L.119 pi-Stacking: D:Y.27, D:Y.27 CRM.10: 14 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 Ligands: PO4.8 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.61, E:S.62, E:W.63, E:E.64, E:V.86, E:I.88, D:L.119 pi-Stacking: E:Y.27, E:Y.27 CRM.11: 14 residues within 4Å: Chain F: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Chain J: I.118, L.119, W.146 Ligands: PO4.19 8 PLIP interactions: 1 interactions with chain J, 7 interactions with chain F Hydrogen bonds: J:L.119, F:S.62, F:W.63, F:E.64, F:V.86, F:I.88 pi-Stacking: F:Y.27, F:Y.27 CRM.14: 14 residues within 4Å: Chain F: I.118, L.119, W.146 Chain G: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.12 9 PLIP interactions: 8 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:Y.27, G:S.62, G:W.63, G:E.64, G:V.86, G:I.88, F:L.119 pi-Stacking: G:Y.27, G:Y.27 CRM.15: 14 residues within 4Å: Chain G: I.118, L.119, W.146 Chain H: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.13 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:S.62, H:W.63, H:E.64, H:V.86, H:I.88, G:L.119 pi-Stacking: H:Y.27, H:Y.27 CRM.17: 14 residues within 4Å: Chain H: I.118, L.119, W.146 Chain I: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.16 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:S.62, I:W.63, I:E.64, I:V.86, I:I.88, H:L.119 pi-Stacking: I:Y.27, I:Y.27 CRM.20: 14 residues within 4Å: Chain I: I.118, L.119, W.146 Chain J: Y.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94 Ligands: PO4.18 9 PLIP interactions: 8 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:G.61, J:S.62, J:W.63, J:E.64, J:V.86, J:I.88, I:L.119 pi-Stacking: J:Y.27, J:Y.27

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

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

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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