SMTL ID : 4kq6.2 (1 other biounit)

Product complex of lumazine synthase from candida glabrata

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-pentamer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: W.38, N.39, R.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.39, A:R.40 SO4.2: 3 residues within 4Å: Chain A: T.156, M.157, H.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.158 Salt bridges: A:H.158 SO4.3: 5 residues within 4Å: Chain A: G.105, S.106, T.107, H.109 Chain B: R.148 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.106, A:T.107, A:T.107 Water bridges: A:T.107, A:F.110, B:R.148 Salt bridges: B:R.148 SO4.4: 3 residues within 4Å: Chain B: W.38, N.39, R.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.39, B:R.40 Water bridges: B:V.41 SO4.5: 3 residues within 4Å: Chain B: T.156, M.157, H.158 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.158 SO4.6: 5 residues within 4Å: Chain B: G.105, S.106, T.107, H.109 Chain C: R.148 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.105, B:S.106, B:T.107, B:T.107 Salt bridges: C:R.148 SO4.8: 6 residues within 4Å: Chain C: G.105, S.106, T.107, H.109 Chain D: R.148, M.157 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.107, C:T.107 Water bridges: C:G.105, C:T.107, C:F.110 Salt bridges: D:R.148 SO4.9: 3 residues within 4Å: Chain C: W.38, N.39, R.40 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.39, C:R.40 Water bridges: C:V.41 SO4.10: 3 residues within 4Å: Chain D: M.157, H.158, H.160 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.158 SO4.11: 5 residues within 4Å: Chain D: G.105, S.106, T.107 Chain E: R.148 Ligands: DLZ.13 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.105, D:S.106, D:T.107 Water bridges: D:F.110 Salt bridges: E:R.148 SO4.14: 4 residues within 4Å: Chain E: R.37, W.38, N.39, R.40 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.39, E:R.40 SO4.15: 5 residues within 4Å: Chain A: R.148 Chain E: G.105, S.106, T.107, H.109 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.106, E:T.107, E:T.107 Water bridges: E:G.105, E:F.110, A:H.160 Salt bridges: A:R.148 SO4.16: 3 residues within 4Å: Chain E: K.28, R.30, N.63 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.28, E:N.63 Water bridges: E:R.30 Salt bridges: E:R.30

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain B: G.71, S.72, F.73, E.74, H.109 Chain C: I.133, F.134 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:F.73, C:F.134, C:F.134 Water bridges: B:S.72 GOL.12: 6 residues within 4Å: Chain C: G.71, F.73, E.74 Chain D: I.133, F.134, W.164 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:F.134, D:F.134, C:E.74 Water bridges: D:L.136, C:S.72 GOL.17: 7 residues within 4Å: Chain A: I.133, F.134, W.164 Chain E: G.71, F.73, E.74, H.109 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:F.134, A:F.134, E:E.74 Water bridges: A:L.136, E:S.72

1 x DLZ: 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol(Non-covalent)

DLZ.13: 14 residues within 4Å: Chain D: W.38, G.71, S.72, F.73, E.74, V.101, L.102, I.103, H.109, I.113 Chain E: I.133, F.134, W.164 Ligands: SO4.11 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:W.38 Hydrogen bonds: D:S.72, D:F.73, D:E.74, D:V.101, D:V.101, D:I.103, E:F.134 Water bridges: D:W.38 pi-Stacking: D:W.38, D:W.38, D:W.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shankar, M. et al., Catalysis product captured in lumazine synthase from the fungal pathogen Candida glabrata. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-05-29

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

6,7-dimethyl-8-ribityllumazine synthase

Related Entries With Identical Sequence