SMTL ID : 1y1s.1

Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Uracil and Sulfate Ion at 2.55A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: G.26, D.27, R.30, R.91, I.92, G.93, T.94, E.198 Chain D: R.48 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.26, A:D.27, A:I.92, A:T.94 Water bridges: A:R.91, A:T.94 Salt bridges: A:R.30, A:R.91, D:R.48 SO4.3: 5 residues within 4Å: Chain B: G.26, R.91, I.92, G.93, T.94 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:G.26, B:I.92, B:T.94 Water bridges: B:R.91, B:R.91 Salt bridges: B:R.91, E:R.48 SO4.4: 7 residues within 4Å: Chain C: G.26, R.30, R.91, I.92, G.93, T.94 Chain F: R.48 7 PLIP interactions: 1 interactions with chain F, 6 interactions with chain C Salt bridges: F:R.48, C:R.30, C:R.91 Hydrogen bonds: C:G.26, C:D.27, C:T.94, C:T.94 SO4.6: 8 residues within 4Å: Chain A: R.48 Chain D: G.26, D.27, R.91, I.92, G.93, T.94, E.198 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.26, D:D.27, D:T.94, D:T.94 Water bridges: D:R.91 Salt bridges: D:R.91, A:R.48 SO4.8: 8 residues within 4Å: Chain B: R.48 Chain E: G.26, D.27, R.30, R.91, I.92, G.93, T.94 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain E Salt bridges: B:R.48, E:R.30, E:R.91 Hydrogen bonds: E:G.26, E:D.27, E:T.94 Water bridges: E:T.94, E:E.198 SO4.10: 8 residues within 4Å: Chain C: R.48 Chain F: G.26, D.27, R.91, I.92, G.93, T.94, E.198 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:G.26, F:D.27, F:I.92, F:T.94 Salt bridges: F:R.91, C:R.48

5 x URA: URACIL(Non-covalent)

URA.2: 11 residues within 4Å: Chain A: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.220 Hydrogen bonds: A:T.94, A:G.96, A:Q.166, A:Q.166, A:R.168, A:R.168 Water bridges: A:M.197 URA.5: 11 residues within 4Å: Chain C: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.220 Hydrogen bonds: C:T.94, C:Q.166, C:Q.166, C:R.168 URA.7: 10 residues within 4Å: Chain D: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, V.221 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.94, D:Q.166, D:Q.166, D:R.168, D:R.168 Water bridges: D:M.197, D:M.197 URA.9: 10 residues within 4Å: Chain E: T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:V.221 Hydrogen bonds: E:Q.166, E:Q.166, E:R.168 Water bridges: E:T.94, E:M.197 URA.11: 11 residues within 4Å: Chain F: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.162, F:I.220 Hydrogen bonds: F:T.94, F:G.96, F:Q.166, F:Q.166, F:R.168, F:R.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabdoulkhakov, A.G. et al., Crystal Structures of Salmonella Typhimurium Uridine Phosphorylase in Native and Three Complexes Forms - with Uridine, Uracil and Sulfate. To be Published

Release Date

2005-11-22

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
F

E
E

F
B

Uridine phosphorylase

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