SMTL ID : 2f59.1 (1 other biounit)

Lumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, Swiss-Prot entry Q57DY1) complexed with inhibitor 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-pentamer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: A.67, E.73 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.67, A:E.73 CA.2: 1 residues within 4Å: Chain A: E.124 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.124, A:E.124 CA.4: 2 residues within 4Å: Chain B: A.67, E.73 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.67, B:E.73 CA.6: 2 residues within 4Å: Chain C: A.67, E.73 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.67, C: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: 2 residues within 4Å: Chain D: D.25, D.28 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.28

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

INI.3: 19 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, F.91, V.94 Chain E: G.114, N.115, K.137, F.140, A.144 12 PLIP interactions: 4 interactions with chain E, 8 interactions with chain A Hydrogen bonds: E:I.113, E:N.115, E:K.137, E:K.137, A:P.51, A:A.53, A:L.54, A:T.82, A:I.84 Water bridges: A:F.22, A:F.22 pi-Stacking: A:F.22 INI.5: 19 residues within 4Å: Chain A: G.114, N.115, K.137, F.140, A.144 Chain B: A.20, F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, F.91, V.94 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:P.51, B:A.53, B:L.54, B:T.82, B:I.84, A:I.113, A:N.115, A:K.137 Water bridges: B:T.82 pi-Stacking: B:F.22 INI.8: 20 residues within 4Å: Chain B: I.113, G.114, N.115, K.137, F.140, A.144 Chain C: A.20, F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, F.91, V.94 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:I.113, B:N.115, B:K.137, C:Y.23, C:P.51, C:A.53, C:L.54, C:T.82, C:I.84 Water bridges: C:F.22, C:F.22, C:E.55 pi-Stacking: C:F.22 INI.10: 20 residues within 4Å: Chain C: I.113, G.114, N.115, K.137, 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, F.91, V.94 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:P.51, D:A.53, D:L.54, D:T.82, D:I.84, C:I.113, C:N.115, C:K.137 Water bridges: D:F.22, D:F.22, D:E.55 pi-Stacking: D:F.22 INI.11: 19 residues within 4Å: Chain D: G.114, N.115, K.137, F.140, A.144 Chain E: A.20, F.22, Y.23, P.51, G.52, A.53, L.54, E.55, T.82, V.83, I.84, H.90, F.91, V.94 12 PLIP interactions: 8 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:P.51, E:A.53, E:L.54, E:T.82, E:I.84, D:I.113, D:N.115, D:K.137, D:K.137 Water bridges: E:F.22, E:E.55 pi-Stacking: E: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

2006-11-28

Peptides

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

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