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

Lumazine Synthase from S.pombe bound to carboxyethyllumazine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-10-mer

Ligands

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

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.3: 16 residues within 4Å: Chain A: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Chain E: I.118, L.119, W.146 Ligands: PO4.1 14 PLIP interactions: 2 interactions with chain E, 12 interactions with chain A Hydrogen bonds: E:L.119, A:S.62, A:W.63, A:E.64, A:V.86, A:I.88 Water bridges: E:L.121, A:W.27, A:V.86, A:T.92 Hydrophobic interactions: A:W.27 Salt bridges: A:H.94 pi-Stacking: A:W.27, A:W.27 CRM.4: 16 residues within 4Å: Chain A: I.118, L.119, W.146 Chain B: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Ligands: PO4.2 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.27 Hydrogen bonds: B:S.62, B:W.63, B:E.64, B:V.86, B:I.88, A:L.119 Water bridges: B:V.86, B:V.86, B:G.90 Salt bridges: B:H.94 pi-Stacking: B:W.27, B:W.27 CRM.6: 16 residues within 4Å: Chain B: I.118, L.119, W.146 Chain C: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Ligands: PO4.5 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.27, C:H.94 Hydrogen bonds: C:S.62, C:W.63, C:E.64, C:V.86, C:I.88, B:L.119 Water bridges: C:W.27, C:V.86, C:G.90, B:L.121 Salt bridges: C:H.94 pi-Stacking: C:W.27, C:W.27 CRM.8: 16 residues within 4Å: Chain C: I.118, L.119, W.146 Chain D: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Ligands: PO4.7 13 PLIP interactions: 1 interactions with chain C, 12 interactions with chain D Hydrogen bonds: C:L.119, D:S.62, D:W.63, D:E.64, D:V.86, D:I.88, D:F.95 Hydrophobic interactions: D:W.27 Water bridges: D:W.27, D:V.86, D:G.90 Salt bridges: D:H.94 pi-Stacking: D:W.27 CRM.10: 16 residues within 4Å: Chain D: I.118, L.119, W.146 Chain E: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Ligands: PO4.9 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:W.27 Hydrogen bonds: E:S.62, E:W.63, E:E.64, E:V.86, E:I.88, D:L.119 Water bridges: E:W.27, E:V.86, E:T.92 Salt bridges: E:H.94 pi-Stacking: E:W.27, E:W.27 CRM.13: 16 residues within 4Å: Chain F: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Chain J: I.118, L.119, W.146 Ligands: PO4.11 14 PLIP interactions: 2 interactions with chain J, 12 interactions with chain F Hydrogen bonds: J:L.119, F:S.62, F:W.63, F:E.64, F:V.86, F:I.88 Water bridges: J:L.121, F:W.27, F:V.86, F:G.90 Hydrophobic interactions: F:W.27 Salt bridges: F:H.94 pi-Stacking: F:W.27, F:W.27 CRM.14: 16 residues within 4Å: Chain F: I.118, L.119, W.146 Chain G: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Ligands: PO4.12 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:W.27 Hydrogen bonds: G:S.62, G:W.63, G:E.64, G:V.86, G:I.88, F:L.119 Water bridges: G:V.86, G:V.86, G:G.90 Salt bridges: G:H.94 pi-Stacking: G:W.27, G:W.27 CRM.16: 16 residues within 4Å: Chain G: I.118, L.119, W.146 Chain H: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Ligands: PO4.15 15 PLIP interactions: 13 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:W.27, H:H.94 Hydrogen bonds: H:S.62, H:W.63, H:E.64, H:V.86, H:I.88, G:L.119 Water bridges: H:W.27, H:V.86, H:G.90, G:L.121 Salt bridges: H:H.94 pi-Stacking: H:W.27, H:W.27 CRM.18: 16 residues within 4Å: Chain H: I.118, L.119, W.146 Chain I: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Ligands: PO4.17 13 PLIP interactions: 12 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:W.27 Hydrogen bonds: I:S.62, I:W.63, I:E.64, I:V.86, I:I.88, I:F.95, H:L.119 Water bridges: I:W.27, I:V.86, I:G.90 Salt bridges: I:H.94 pi-Stacking: I:W.27 CRM.20: 16 residues within 4Å: Chain I: I.118, L.119, W.146 Chain J: W.27, N.28, G.61, S.62, W.63, E.64, V.86, L.87, I.88, H.94, F.95, I.98 Ligands: PO4.19 13 PLIP interactions: 12 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:W.27 Hydrogen bonds: J:S.62, J:W.63, J:E.64, J:V.86, J:I.88, I:L.119 Water bridges: J:W.27, J:V.86, J:T.92 Salt bridges: J:H.94 pi-Stacking: J:W.27, J:W.27

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: 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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