SMTL ID : 4g3m.1

Complex Structure of Bacillus subtilis RibG: The Deamination Process in Riboflavin Biosynthesis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.61, E.63, C.86, C.95 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.61, A:C.86, A:C.95 ZN.3: 4 residues within 4Å: Chain B: H.61, C.86, C.95 Ligands: AOF.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.61, B:C.86, B:C.95 ZN.6: 4 residues within 4Å: Chain C: H.61, C.86, C.95 Ligands: AOF.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.61, C:C.86, C:C.95 ZN.9: 4 residues within 4Å: Chain D: H.61, C.86, C.95 Ligands: AOF.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.61, D:C.86, D:C.95

4 x AI9: [(2R,3S,4S,5E)-5-[[5-azanyl-2,4-bis(oxidanylidene)-1H-pyrimidin-6-yl]imino]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate(Non-covalent)

AI9.2: 17 residues within 4Å: Chain A: K.163, A.165, S.179, W.181, I.182, T.183, R.188, R.195, T.207, D.211, P.213, S.214, L.215, T.216, R.218, E.302, G.303 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.163, A:K.163, A:S.179, A:W.181, A:I.182, A:T.183, A:T.183, A:R.195, A:D.211, A:S.214, A:S.214, A:L.215, A:T.216, A:G.303 Water bridges: A:S.179, A:S.179, A:R.218 Salt bridges: A:R.195, A:R.218 pi-Stacking: A:W.181 AI9.5: 14 residues within 4Å: Chain B: K.163, A.165, S.179, I.182, T.183, R.188, R.195, D.211, P.213, S.214, L.215, T.216, R.218, E.302 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.163, B:K.163, B:S.179, B:I.182, B:T.183, B:T.183, B:T.183, B:R.195, B:S.214, B:L.215, B:T.216, B:E.302 Water bridges: B:R.218, B:R.218 Salt bridges: B:R.195, B:R.218 AI9.8: 14 residues within 4Å: Chain C: K.163, A.165, S.179, W.181, I.182, T.183, R.188, R.195, D.211, P.213, S.214, L.215, R.218, E.302 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:K.163, C:K.163, C:S.179, C:I.182, C:T.183, C:T.183, C:T.183, C:R.195, C:D.211, C:S.214, C:S.214, C:L.215 Salt bridges: C:R.195, C:R.218 AI9.11: 15 residues within 4Å: Chain D: K.163, A.165, S.179, I.182, T.183, R.188, R.195, T.207, D.211, P.213, S.214, L.215, T.216, R.218, E.302 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:K.163, D:K.163, D:S.179, D:I.182, D:T.183, D:T.183, D:R.188, D:R.195, D:D.211, D:S.214, D:S.214, D:L.215, D:T.216 Salt bridges: D:R.195, D:R.218

3 x AOF: N-(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)-5-O-phosphono-beta-D-ribofuranosylamine(Non-covalent)

AOF.4: 18 residues within 4Å: Chain B: N.35, P.36, V.38, H.54, H.61, A.62, E.63, E.84, C.86, H.88, G.90, K.91, T.92, C.95, D.113, N.115, F.149 Ligands: ZN.3 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:H.54, B:A.62, B:E.63, B:C.86, B:K.91, B:T.92, B:T.92, B:T.92, B:N.115 Water bridges: B:D.113, B:D.113 Salt bridges: B:H.61, B:H.88, B:K.91 pi-Stacking: B:H.61 AOF.7: 16 residues within 4Å: Chain C: N.35, P.36, V.38, H.54, H.61, A.62, E.63, C.86, H.88, G.90, K.91, T.92, C.95, D.113, F.149 Ligands: ZN.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.35, C:A.62, C:E.63, C:C.86, C:G.90, C:K.91, C:T.92, C:N.115 Water bridges: C:N.35 Salt bridges: C:H.61, C:K.91 pi-Stacking: C:H.61 AOF.10: 18 residues within 4Å: Chain D: N.35, P.36, V.38, H.54, H.61, A.62, E.63, E.84, P.85, C.86, H.88, G.90, K.91, T.92, C.95, D.113, F.149 Ligands: ZN.9 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:P.36, D:A.62, D:E.63, D:E.84, D:C.86, D:G.90, D:K.91, D:T.92 Water bridges: D:N.35, D:T.92 Salt bridges: D:H.61, D:H.88, D:K.91 pi-Stacking: D:H.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S.C. et al., Evolution of vitamin B(2) biosynthesis: eubacterial RibG and fungal Rib2 deaminases. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-02-20

Peptides

Riboflavin biosynthesis protein RibD: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Riboflavin biosynthesis protein RibD

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