SMTL ID : 4yjk.1

Crystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-hexamer

Ligands

3 x URA: URACIL(Non-covalent)

URA.1: 10 residues within 4Å: Chain A: T.92, T.93, G.94, F.160, Q.164, R.166, Y.193, E.194, M.195, V.219 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.92, A:G.94, A:Q.164, A:Q.164, A:R.166, A:R.166 Water bridges: A:T.92, A:M.195 URA.5: 10 residues within 4Å: Chain B: T.92, T.93, G.94, F.160, Q.164, R.166, Y.193, E.194, M.195, V.219 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.160 Hydrogen bonds: B:T.92, B:G.94, B:Q.164, B:Q.164, B:R.166, B:R.166 Water bridges: B:M.195 URA.7: 10 residues within 4Å: Chain C: T.92, T.93, G.94, F.160, Q.164, R.166, Y.193, E.194, M.195, V.219 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.160 Hydrogen bonds: C:G.94, C:Q.164, C:Q.164, C:R.166, C:R.166

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

SO4.2: 9 residues within 4Å: Chain A: P.23, G.24, D.25, R.28, R.89, V.90, G.91, T.92 Chain D: R.46 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.24, A:D.25, A:T.92, A:T.92 Water bridges: A:R.89, A:R.89 Salt bridges: A:R.28, A:R.89, D:R.46 SO4.3: 4 residues within 4Å: Chain A: R.31, S.238, A.239, V.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.238, A:A.239, A:V.240 Salt bridges: A:R.31 SO4.4: 3 residues within 4Å: Chain A: R.176 Chain B: R.176 Chain F: R.176 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F, 2 interactions with chain B Salt bridges: A:R.176, F:R.176, B:R.176 Water bridges: F:R.176, B:R.176 SO4.6: 8 residues within 4Å: Chain B: G.24, D.25, R.28, R.89, V.90, G.91, T.92 Chain E: R.46 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:G.24, B:D.25, B:T.92 Water bridges: B:T.92, B:T.92, B:E.196 Salt bridges: B:R.28, B:R.89, E:R.46 SO4.8: 9 residues within 4Å: Chain C: P.23, G.24, D.25, R.28, R.89, V.90, G.91, T.92 Chain F: R.46 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.24, C:D.25, C:T.92 Water bridges: C:T.92, C:T.92, C:E.194 Salt bridges: C:R.28, C:R.89, F:R.46 SO4.9: 7 residues within 4Å: Chain A: R.46 Chain D: G.24, R.28, R.89, V.90, G.91, T.92 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.24, D:T.92, D:T.92 Water bridges: D:R.28, D:R.89 Salt bridges: D:R.28, D:R.89, A:R.46 SO4.10: 3 residues within 4Å: Chain C: R.176 Chain D: R.176 Chain E: R.176 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D, 1 interactions with chain E Water bridges: C:R.176, C:R.176, D:R.176 Salt bridges: C:R.176, D:R.176, E:R.176 SO4.11: 4 residues within 4Å: Chain B: R.46 Chain E: R.28, G.91, T.92 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain E Salt bridges: B:R.46, E:R.28 Hydrogen bonds: E:G.24, E:T.92 SO4.12: 7 residues within 4Å: Chain C: R.46 Chain F: G.24, R.28, R.89, V.90, G.91, T.92 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:G.24, F:T.92 Water bridges: F:R.28, C:R.46 Salt bridges: F:R.28, F:R.89, C:R.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safonova, T.N. et al., Concerted action of two subunits of the functional dimer of Shewanella oneidensis MR-1 uridine phosphorylase derived from a comparison of the C212S mutant and the wild-type enzyme. Acta Crystallogr D Struct Biol (2016)

Release Date

2015-03-11

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

C
A

D
C

E
E

F
B

Uridine phosphorylase