SMTL ID : 1rxc.1 (1 other biounit)

E. COLI uridine phosphorylase: 5-fluorouracil ribose-1-phosphate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-hexamer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: E.49, I.69, S.73 Chain B: E.49, I.69, S.73 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.49, A:I.69, A:S.73, B:E.49, B:I.69 K.5: 6 residues within 4Å: Chain C: E.49, I.69, S.73 Chain D: E.49, I.69, S.73 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Metal complexes: D:E.49, D:I.69, C:E.49, C:I.69, C:S.73 K.10: 6 residues within 4Å: Chain E: E.49, I.69, S.73 Chain F: E.49, I.69, S.73 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Metal complexes: E:E.49, E:I.69, E:S.73, F:E.49, F:I.69

5 x R1P: 1-O-phosphono-alpha-D-ribofuranose(Non-covalent)

R1P.2: 14 residues within 4Å: Chain A: H.8, R.48 Chain B: G.26, R.30, I.69, R.91, I.92, G.93, T.94, F.162, E.196, M.197, E.198 Ligands: URF.3 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.26, B:T.94, B:T.94, B:E.196, B:E.196, B:M.197, B:E.198, A:H.8 Salt bridges: B:R.30, B:R.91, B:R.91, A:R.48, A:R.48 Water bridges: A:R.48, A:R.48 R1P.4: 14 residues within 4Å: Chain C: G.26, R.30, I.69, R.91, I.92, G.93, T.94, F.162, E.196, M.197, E.198 Chain D: H.8, R.48 Ligands: URF.6 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.26, C:T.94, C:T.94, C:E.196, C:E.196, C:M.197, D:H.8 Water bridges: C:E.198, C:E.198 Salt bridges: C:R.30, C:R.91, D:R.48, D:R.48 R1P.7: 14 residues within 4Å: Chain C: H.8, R.48 Chain D: G.26, R.30, I.69, R.91, I.92, G.93, T.94, F.162, E.196, M.197, E.198 Ligands: URF.8 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.26, D:T.94, D:T.94, D:E.196, D:E.196, D:M.197, D:E.198, C:H.8 Water bridges: D:R.91, D:R.91, C:R.48 Salt bridges: D:R.30, D:R.91, C:R.48, C:R.48 R1P.9: 14 residues within 4Å: Chain E: G.26, R.30, I.69, R.91, I.92, G.93, T.94, F.162, E.196, M.197, E.198 Chain F: H.8, R.48 Ligands: URF.11 15 PLIP interactions: 10 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:G.26, E:R.91, E:T.94, E:T.94, E:E.196, E:M.197, E:E.198, F:H.8 Salt bridges: E:R.30, E:R.91, E:R.91, F:R.48, F:R.48 Water bridges: F:R.48, F:R.48 R1P.12: 14 residues within 4Å: Chain E: H.8, R.48 Chain F: G.26, R.30, I.69, R.91, I.92, G.93, T.94, F.162, E.196, M.197, E.198 Ligands: URF.13 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:G.26, F:R.91, F:T.94, F:T.94, F:M.197, E:H.8 Salt bridges: F:R.30, F:R.91, F:R.91, E:R.48, E:R.48

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

URF.3: 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: R1P.2 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.94, B:G.96, B:Q.166, B:Q.166, B:R.168, B:R.168 Water bridges: B:T.94 pi-Stacking: B:F.162 URF.6: 12 residues within 4Å: Chain C: T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, I.220, V.221, P.229 Ligands: R1P.4 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.94, C:Q.166, C:Q.166, C:R.168, C:R.168 URF.8: 13 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 Ligands: R1P.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.94, D:G.96, D:Q.166, D:Q.166, D:R.168, D:R.168 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: R1P.9 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:T.94, E:G.96, E:Q.166, E:Q.166, E:R.168, E:R.168 Water bridges: E:T.94 pi-Stacking: E:F.162 URF.13: 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: R1P.12 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caradoc-Davies, T.T. et al., Crystal structures of escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium. J.Mol.Biol. (2004)

Release Date

2004-04-13

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Uridine phosphorylase

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