SMTL ID : 4e1v.1 (1 other biounit)

X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with 5-Fluorouracil at 2.15 A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

6 x URF: 5-FLUOROURACIL(Non-covalent)

URF.1: 13 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, P.229 Ligands: GOL.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.94, A:Q.166, A:Q.166, A:R.168, A:R.168 URF.4: 13 residues within 4Å: Chain B: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221, P.229 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.94, B:G.96, B:Q.166, B:Q.166, B:R.168, B:R.168 URF.7: 12 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 Ligands: GOL.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.96, C:Q.166, C:Q.166, C:R.168, C:R.168 URF.9: 12 residues within 4Å: Chain D: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221, P.229 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.94, D:G.96, D:Q.166, D:Q.166, D:R.168, D:R.168 Water bridges: D:T.94 URF.11: 13 residues within 4Å: Chain E: T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221, P.229 Ligands: GOL.13 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.94, E:Q.166, E:Q.166, E:R.168, E:R.168 URF.14: 13 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, P.229 Ligands: GOL.15 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:T.94, F:G.96, F:Q.166, F:Q.166, F:R.168, F:R.168

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: T.94, E.196, M.197, E.198 Chain F: H.8, R.48 Ligands: URF.1 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:T.94, A:T.94, A:M.197, A:E.198, F:H.8 Water bridges: A:T.94, A:E.198, F:R.48 GOL.5: 5 residues within 4Å: Chain B: T.94, E.196, M.197, E.198 Ligands: URF.4 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:H.8, B:T.94, B:M.197, B:E.198 Water bridges: C:R.48, B:T.94 GOL.8: 7 residues within 4Å: Chain B: H.8, R.48 Chain C: T.94, E.196, M.197, E.198 Ligands: URF.7 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.94, C:T.94, C:M.197, B:R.48, B:R.48 Water bridges: C:T.94 GOL.13: 7 residues within 4Å: Chain D: H.8, R.48 Chain E: T.94, E.196, M.197, E.198 Ligands: URF.11 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:H.8, E:T.94, E:M.197, E:E.198 Water bridges: D:R.48, E:R.91 GOL.15: 5 residues within 4Å: Chain F: T.94, E.196, M.197, E.198 Ligands: URF.14 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain F Hydrogen bonds: A:H.8, F:T.94, F:T.94, F:M.197, F:E.198

3 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: E.49, I.69, S.73 Chain F: E.49, I.69, S.73 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Metal complexes: F:E.49, A:E.49 K.6: 6 residues within 4Å: Chain B: E.49, I.69, S.73 Chain C: E.49, I.69, S.73 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:E.49, B:E.49 K.10: 6 residues within 4Å: Chain D: E.49, I.69, S.73 Chain E: E.49, I.69, S.73 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Metal complexes: E:E.49, D:E.49

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 3 residues within 4Å: Chain D: L.121, P.125 Chain E: R.179 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lashkov, A.A. et al., X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae. Acta Crystallogr.,Sect.D (2012)

Release Date

2013-03-06

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
F

D
D

E
C

F
B

Uridine phosphorylase

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