SMTL ID : 2rj3.1

Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Uracil and Phosphate Ion at 2.49A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: G.25, D.26, R.29, R.90, I.91, G.92, T.93, E.197 Chain D: R.47 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.25, A:D.26, A:I.91, A:T.93 Water bridges: A:R.90 Salt bridges: A:R.29, A:R.90, D:R.47 PO4.3: 7 residues within 4Å: Chain B: G.25, R.90, I.91, G.92, T.93, E.197 Chain E: R.47 8 PLIP interactions: 1 interactions with chain E, 7 interactions with chain B Salt bridges: E:R.47, B:R.90 Hydrogen bonds: B:G.25, B:I.91, B:T.93, B:T.93 Water bridges: B:R.90, B:R.90 PO4.4: 8 residues within 4Å: Chain C: G.25, R.29, R.90, I.91, G.92, T.93, E.197 Chain F: R.47 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.25, C:D.26, C:T.93, C:T.93 Salt bridges: C:R.29, C:R.90, F:R.47 PO4.6: 8 residues within 4Å: Chain A: R.47 Chain D: G.25, D.26, R.90, I.91, G.92, T.93, E.197 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain D Salt bridges: A:R.47, D:R.90 Hydrogen bonds: D:G.25, D:D.26, D:T.93, D:T.93, D:E.197 PO4.8: 8 residues within 4Å: Chain B: R.47 Chain E: G.25, D.26, R.29, R.90, I.91, G.92, T.93 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:G.25, E:D.26, E:T.93 Water bridges: E:T.93, E:E.197 Salt bridges: E:R.29, E:R.90, B:R.47 PO4.10: 8 residues within 4Å: Chain C: R.47 Chain F: G.25, D.26, R.90, I.91, G.92, T.93, E.197 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:G.25, F:D.26, F:I.91, F:T.93, F:T.93 Salt bridges: F:R.90, C:R.47

5 x URA: URACIL(Non-covalent)

URA.2: 11 residues within 4Å: Chain A: T.93, T.94, G.95, F.161, Q.165, R.167, Y.194, E.195, M.196, I.219, V.220 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.93, A:G.95, A:Q.165, A:Q.165, A:R.167, A:R.167 Water bridges: A:M.196 URA.5: 11 residues within 4Å: Chain C: T.93, T.94, G.95, F.161, Q.165, R.167, Y.194, E.195, M.196, I.219, V.220 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.161, C:I.219 Hydrogen bonds: C:T.93, C:G.95, C:Q.165, C:Q.165, C:R.167 URA.7: 11 residues within 4Å: Chain D: T.93, T.94, G.95, F.161, Q.165, R.167, Y.194, E.195, M.196, I.219, V.220 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.219 Hydrogen bonds: D:T.93, D:Q.165, D:Q.165, D:R.167, D:R.167 Water bridges: D:M.196 URA.9: 10 residues within 4Å: Chain E: T.93, T.94, G.95, F.161, Q.165, R.167, Y.194, E.195, M.196, V.220 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:T.93, E:Q.165, E:Q.165, E:R.167, E:R.167 Water bridges: E:M.196 URA.11: 11 residues within 4Å: Chain F: T.93, T.94, G.95, F.161, Q.165, R.167, Y.194, E.195, M.196, I.219, V.220 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.161, F:I.219 Hydrogen bonds: F:T.93, F:G.95, F:Q.165, F:Q.165, F:R.167, F:R.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with Uracil and Phosphate Ion at 2.49A Resolution. To be published

Release Date

2008-10-14

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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