SMTL ID : 1t13.1

Crystal Structure Of Lumazine Synthase From Brucella Abortus Bound To 5-nitro-6-(D-ribitylamino)-2,4(1H,3H) pyrimidinedione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-10-mer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: I.80, D.81, G.82, G.83, I.84, Y.85 Chain E: H.117 Ligands: INI.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.80, A:D.81, A:G.82, A:I.84, A:Y.85 PO4.3: 8 residues within 4Å: Chain A: H.117 Chain B: I.80, D.81, G.82, G.83, I.84, Y.85 Ligands: INI.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.81, B:G.82, B:I.84, B:Y.85 PO4.5: 8 residues within 4Å: Chain C: I.80, D.81, G.82, G.83, I.84, Y.85, R.86 Ligands: INI.6 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.81, C:G.82, C:G.82, C:G.83, C:I.84, C:Y.85 PO4.7: 6 residues within 4Å: Chain D: D.81, G.82, G.83, I.84, Y.85 Ligands: INI.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.82, D:G.82, D:G.82, D:I.84, D:Y.85 PO4.9: 8 residues within 4Å: Chain D: H.117 Chain E: I.80, D.81, G.82, G.83, I.84, Y.85 Ligands: INI.10 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:I.80, E:G.82, E:G.82, E:I.84, E:Y.85 PO4.11: 8 residues within 4Å: Chain F: I.80, D.81, G.82, G.83, I.84, Y.85 Chain J: H.117 Ligands: INI.12 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:I.80, F:D.81, F:D.81, F:G.82, F:I.84, F:Y.85 PO4.13: 8 residues within 4Å: Chain F: H.117 Chain G: I.80, D.81, G.82, G.83, I.84, Y.85 Ligands: INI.14 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:G.82, G:I.84, G:Y.85 PO4.15: 8 residues within 4Å: Chain H: I.80, D.81, G.82, G.83, I.84, Y.85, R.86 Ligands: INI.16 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:G.82, H:G.82, H:G.83, H:I.84, H:Y.85 PO4.17: 6 residues within 4Å: Chain I: D.81, G.82, G.83, I.84, Y.85 Ligands: INI.18 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:D.81, I:G.82, I:G.82, I:G.82, I:I.84, I:Y.85 PO4.19: 8 residues within 4Å: Chain I: H.117 Chain J: I.80, D.81, G.82, G.83, I.84, Y.85 Ligands: INI.20 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:I.80, J:D.81, J:G.82, J:G.82, J:I.84, J:Y.85

10 x INI: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE(Non-covalent)

INI.2: 13 residues within 4Å: Chain A: A.18, W.20, H.21, G.53, A.54, Y.55, E.56, F.78, V.79, I.80 Chain E: L.110, S.111 Ligands: PO4.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:W.20, A:A.54, A:Y.55, A:F.78, A:I.80, A:I.80, E:S.111 Water bridges: A:W.20, A:W.20 pi-Stacking: A:W.20 INI.4: 13 residues within 4Å: Chain A: L.110, S.111 Chain B: A.18, W.20, G.53, A.54, Y.55, E.56, A.77, F.78, V.79, I.80 Ligands: PO4.3 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.20, B:W.20, B:A.54, B:Y.55, B:F.78, B:I.80, B:I.80, A:S.111 Water bridges: B:W.20, B:W.20 pi-Stacking: B:W.20 INI.6: 13 residues within 4Å: Chain B: L.110, S.111 Chain C: A.18, W.20, G.53, A.54, Y.55, E.56, F.78, V.79, I.80, V.90 Ligands: PO4.5 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:W.20, C:A.54, C:Y.55, C:F.78, C:I.80, C:I.80, B:S.111 pi-Stacking: C:W.20, C:W.20 INI.8: 12 residues within 4Å: Chain C: L.110, S.111 Chain D: A.18, W.20, G.53, A.54, Y.55, E.56, F.78, V.79, I.80 Ligands: PO4.7 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:W.20, D:A.54, D:Y.55, D:F.78, D:I.80, D:I.80, C:S.111 pi-Stacking: D:W.20 INI.10: 12 residues within 4Å: Chain D: L.110, S.111 Chain E: A.18, W.20, G.53, A.54, Y.55, E.56, F.78, V.79, I.80 Ligands: PO4.9 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:W.20, E:W.20, E:A.54, E:Y.55, E:F.78, E:I.80, E:I.80, D:S.111 Water bridges: E:F.78, D:K.136 pi-Stacking: E:W.20 INI.12: 13 residues within 4Å: Chain F: A.18, W.20, H.21, G.53, A.54, Y.55, E.56, F.78, V.79, I.80 Chain J: L.110, S.111 Ligands: PO4.11 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:W.20, F:A.54, F:Y.55, F:F.78, F:I.80, F:I.80, J:S.111 Water bridges: F:W.20, F:W.20 pi-Stacking: F:W.20 INI.14: 13 residues within 4Å: Chain F: L.110, S.111 Chain G: A.18, W.20, G.53, A.54, Y.55, E.56, A.77, F.78, V.79, I.80 Ligands: PO4.13 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:W.20, G:W.20, G:A.54, G:Y.55, G:F.78, G:I.80, G:I.80, F:S.111 Water bridges: G:W.20, G:W.20 pi-Stacking: G:W.20 INI.16: 13 residues within 4Å: Chain G: L.110, S.111 Chain H: A.18, W.20, G.53, A.54, Y.55, E.56, F.78, V.79, I.80, V.90 Ligands: PO4.15 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:W.20, H:A.54, H:Y.55, H:F.78, H:I.80, H:I.80, G:S.111 pi-Stacking: H:W.20, H:W.20 INI.18: 12 residues within 4Å: Chain H: L.110, S.111 Chain I: A.18, W.20, G.53, A.54, Y.55, E.56, F.78, V.79, I.80 Ligands: PO4.17 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:W.20, I:A.54, I:Y.55, I:F.78, I:I.80, I:I.80, H:S.111 pi-Stacking: I:W.20 INI.20: 12 residues within 4Å: Chain I: L.110, S.111 Chain J: A.18, W.20, G.53, A.54, Y.55, E.56, F.78, V.79, I.80 Ligands: PO4.19 11 PLIP interactions: 2 interactions with chain I, 9 interactions with chain J Hydrogen bonds: I:S.111, J:W.20, J:W.20, J:A.54, J:Y.55, J:F.78, J:I.80, J:I.80 Water bridges: I:K.136, J:F.78 pi-Stacking: J:W.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klinke, S. et al., Crystallographic studies on Decameric Brucella spp. Lumazine Synthase: A Novel Quaternary Arrangement Evolved for a New Function?. J.Mol.Biol. (2005)

Release Date

2005-04-19

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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