SMTL ID : 1xn1.1

Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-10-mer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: W.20, G.53, A.54, V.79 Ligands: PO4.2 Ligand excluded by PLIP PO4.2: 5 residues within 4Å: Chain A: Y.85, R.86, H.87 Ligands: PO4.1, PO4.20 Ligand excluded by PLIP PO4.5: 5 residues within 4Å: Chain B: W.20, G.53, A.54, F.78, V.79 Ligand excluded by PLIP PO4.6: 5 residues within 4Å: Chain A: H.132, K.136 Chain B: G.82, I.84, Y.85 Ligand excluded by PLIP PO4.10: 5 residues within 4Å: Chain C: W.20, G.53, A.54, F.78, V.79 Ligand excluded by PLIP PO4.11: 5 residues within 4Å: Chain B: H.132, K.136 Chain C: G.82, I.84, Y.85 Ligand excluded by PLIP PO4.12: 5 residues within 4Å: Chain C: H.132, K.136 Chain D: G.82, I.84, Y.85 Ligand excluded by PLIP PO4.14: 3 residues within 4Å: Chain D: W.20, A.54, V.79 Ligand excluded by PLIP PO4.15: 6 residues within 4Å: Chain D: H.132, K.136 Chain E: G.82, I.84, Y.85 Ligands: PO4.22 Ligand excluded by PLIP PO4.20: 6 residues within 4Å: Chain A: G.82, I.84, Y.85 Chain E: H.132, K.136 Ligands: PO4.2 Ligand excluded by PLIP PO4.21: 5 residues within 4Å: Chain E: W.20, G.53, A.54, Y.55, V.79 Ligand excluded by PLIP PO4.22: 6 residues within 4Å: Chain E: I.80, G.82, Y.85, R.86, H.87 Ligands: PO4.15 Ligand excluded by PLIP PO4.25: 4 residues within 4Å: Chain F: W.20, G.53, A.54, V.79 Ligand excluded by PLIP PO4.26: 5 residues within 4Å: Chain F: G.82, I.84, Y.85 Chain J: H.132, K.136 Ligand excluded by PLIP PO4.28: 4 residues within 4Å: Chain G: W.20, A.54, F.78, V.79 Ligand excluded by PLIP PO4.29: 5 residues within 4Å: Chain F: H.132, K.136 Chain G: G.82, I.84, Y.85 Ligand excluded by PLIP PO4.32: 6 residues within 4Å: Chain H: W.20, G.53, A.54, F.78, V.90 Ligands: PO4.34 Ligand excluded by PLIP PO4.33: 6 residues within 4Å: Chain G: H.132, K.136 Chain H: G.82, I.84, Y.85 Ligands: PO4.34 Ligand excluded by PLIP PO4.34: 4 residues within 4Å: Chain G: K.136 Chain H: W.20 Ligands: PO4.32, PO4.33 Ligand excluded by PLIP PO4.37: 4 residues within 4Å: Chain I: W.20, G.53, A.54, V.79 Ligand excluded by PLIP PO4.38: 6 residues within 4Å: Chain C: E.124 Chain H: H.132, K.136 Chain I: G.82, I.84, Y.85 Ligand excluded by PLIP PO4.42: 6 residues within 4Å: Chain J: W.20, G.53, A.54, F.78, V.79 Ligands: PO4.44 Ligand excluded by PLIP PO4.43: 6 residues within 4Å: Chain I: H.132, K.136 Chain J: G.82, I.84, Y.85 Ligands: PO4.44 Ligand excluded by PLIP PO4.44: 4 residues within 4Å: Chain I: E.139 Chain J: W.20 Ligands: PO4.42, PO4.43 Ligand excluded by PLIP

7 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: E.56 Chain E: L.110, S.111 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.111, A:E.56 NA.4: 3 residues within 4Å: Chain A: L.110, S.111 Chain B: E.56 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.111, B:E.56 NA.9: 2 residues within 4Å: Chain B: I.48, D.50 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.50 NA.19: 2 residues within 4Å: Chain D: S.111 Chain E: E.56 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:E.56, D:S.111 NA.27: 2 residues within 4Å: Chain F: E.56 Chain J: S.111 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain F Hydrogen bonds: J:S.111, F:E.56 NA.31: 3 residues within 4Å: Chain G: L.110, S.111 Chain H: E.56 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.111, G:S.111 NA.46: 5 residues within 4Å: Chain F: V.90 Chain J: I.95, S.111, V.113, L.114 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:S.111, J:S.111

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 2 residues within 4Å: Chain B: R.29, K.30 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.29, B:K.30 SO4.8: 2 residues within 4Å: Chain B: R.151, S.152 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.151 SO4.13: 2 residues within 4Å: Chain C: R.29, K.30 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.29 SO4.16: 3 residues within 4Å: Chain D: E.27, K.30, K.134 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.27 Salt bridges: D:K.30, D:K.134 SO4.17: 2 residues within 4Å: Chain D: R.29, K.30 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.29 SO4.18: 3 residues within 4Å: Chain D: H.142, L.145, Q.146 No protein-ligand interaction detected (PLIP) SO4.23: 2 residues within 4Å: Chain E: R.29, K.30 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.29, E:K.30 SO4.24: 2 residues within 4Å: Chain E: E.106, R.151 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.151 SO4.30: 2 residues within 4Å: Chain G: R.29, K.30 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:R.29 SO4.35: 2 residues within 4Å: Chain H: R.29, K.30 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:R.29 SO4.36: 5 residues within 4Å: Chain H: R.86, D.88, T.92 Chain I: F.89 Ligands: SO4.40 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:R.86, H:T.92, H:T.92, I:R.86 SO4.39: 2 residues within 4Å: Chain I: R.29, K.30 1 PLIP interactions: 1 interactions with chain I Salt bridges: I:R.29 SO4.40: 6 residues within 4Å: Chain I: D.88, T.92 Chain J: R.86, D.88, F.89 Ligands: SO4.36 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:D.88, I:D.88 Salt bridges: J:R.86 SO4.41: 4 residues within 4Å: Chain I: A.65, R.66, T.105, V.107 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.66, I:T.105 SO4.45: 3 residues within 4Å: Chain J: D.26, R.29, K.30 2 PLIP interactions: 2 interactions with chain J Salt bridges: J:R.29, J:K.30

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

2005-09-27

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
F

G
G

H
H

I
I

J
J

6,7-dimethyl-8-ribityllumazine synthase

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