SMTL ID : 2o6h.2 (1 other biounit)

Lumazine synthase RibH1 from Brucella melitensis (Gene BMEI1187, Swiss-Prot entry Q8YGH2) complexed with inhibitor 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-10-mer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: A.67, E.73 Chain J: A.67, E.73 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain A Metal complexes: J:A.67, A:E.73 CA.2: 1 residues within 4Å: Chain A: E.124 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.124 CA.4: 4 residues within 4Å: Chain B: A.67, E.73 Chain I: A.67, E.73 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain B Metal complexes: I:E.73, B:A.67, B:E.73 CA.6: 7 residues within 4Å: Chain C: A.67, G.70, G.71, E.73 Chain H: A.67, E.73 Ligands: CA.17 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain H Metal complexes: C:A.67, H:E.73 CA.7: 1 residues within 4Å: Chain C: E.124 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.124, C:E.124 CA.9: 1 residues within 4Å: Chain D: D.24 No protein-ligand interaction detected (PLIP) CA.12: 4 residues within 4Å: Chain E: A.67, E.73 Chain F: A.67, E.73 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Metal complexes: E:A.67, F:E.73 CA.13: 1 residues within 4Å: Chain F: E.124 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.124 CA.15: 4 residues within 4Å: Chain D: A.67, E.73 Chain G: A.67, E.73 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain D Metal complexes: G:A.67, G:E.73, D:E.73 CA.17: 7 residues within 4Å: Chain C: A.67, E.73 Chain H: A.67, G.70, G.71, E.73 Ligands: CA.6 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain H Metal complexes: C:E.73, H:A.67 CA.18: 1 residues within 4Å: Chain H: E.124 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.124, H:E.124 CA.20: 1 residues within 4Å: Chain I: D.24 No protein-ligand interaction detected (PLIP)

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

INI.3: 15 residues within 4Å: Chain A: A.20, F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 Chain E: N.115, F.140 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Y.23, A:P.51, A:A.53, A:L.54, A:T.82, A:I.84, E:N.115 Water bridges: A:T.82 pi-Stacking: A:F.22 INI.5: 15 residues within 4Å: Chain A: N.115, F.140, A.144 Chain B: F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:N.115, B:A.53, B:L.54, B:T.82, B:I.84 Water bridges: B:T.82 pi-Stacking: B:F.22 INI.8: 16 residues within 4Å: Chain B: G.114, N.115, F.140, A.144 Chain C: F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.53, C:L.54, C:T.82, C:I.84, B:N.115 Water bridges: C:T.82 pi-Stacking: C:F.22 INI.10: 17 residues within 4Å: Chain C: G.114, N.115, F.140, A.144 Chain D: A.20, F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.23, D:A.53, D:L.54, D:T.82, D:I.84, C:N.115 Water bridges: D:E.55, C:I.113 pi-Stacking: D:F.22 INI.11: 15 residues within 4Å: Chain D: G.114, N.115, F.140, A.144 Chain E: F.22, Y.23, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:Y.23, E:A.53, E:L.54, E:T.82, E:I.84, D:N.115 Water bridges: E:H.90, D:K.137 pi-Stacking: E:F.22 INI.14: 15 residues within 4Å: Chain F: A.20, F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 Chain J: N.115, F.140 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain J Hydrogen bonds: F:P.51, F:A.53, F:L.54, F:T.82, F:I.84, J:N.115 Water bridges: F:T.82 pi-Stacking: F:F.22 INI.16: 15 residues within 4Å: Chain F: N.115, F.140, A.144 Chain G: F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 8 PLIP interactions: 1 interactions with chain F, 7 interactions with chain G Hydrogen bonds: F:N.115, G:Y.23, G:A.53, G:L.54, G:T.82, G:I.84 Water bridges: G:T.82 pi-Stacking: G:F.22 INI.19: 16 residues within 4Å: Chain G: G.114, N.115, F.140, A.144 Chain H: F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:Y.23, H:A.53, H:L.54, H:T.82, H:I.84, G:N.115 Water bridges: H:T.82 pi-Stacking: H:F.22 INI.21: 17 residues within 4Å: Chain H: G.114, N.115, F.140, A.144 Chain I: A.20, F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 8 PLIP interactions: 6 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:A.53, I:L.54, I:T.82, I:I.84, H:N.115 Water bridges: I:E.55, H:I.113 pi-Stacking: I:F.22 INI.22: 15 residues within 4Å: Chain I: G.114, N.115, F.140, A.144 Chain J: F.22, Y.23, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, V.94 8 PLIP interactions: 7 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:A.53, J:L.54, J:T.82, J:I.84, I:N.115 Water bridges: J:H.90, J:H.90 pi-Stacking: J:F.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klinke, S. et al., Structural and Kinetic Properties of Lumazine Synthase Isoenzymes in the Order Rhizobiales. J.Mol.Biol. (2007)

Release Date

2007-08-14

Peptides

6,7-dimethyl-8-ribityllumazine synthase 1: 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 1

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