SMTL ID : 1u1f.1

Structure of e. coli uridine phosphorylase complexed to 5-(m-(benzyloxy)benzyl)acyclouridine (BBAU)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: G.29, R.33, R.94, I.95, G.96, T.97, E.201 Chain B: R.51 Ligands: 183.3 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.29, A:T.97, A:E.201 Water bridges: A:R.94, B:R.51 Salt bridges: A:R.33, A:R.94, B:R.51 PO4.4: 9 residues within 4Å: Chain A: R.51 Chain B: G.29, R.33, R.94, I.95, G.96, T.97, E.201 Ligands: 183.5 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.29, B:D.30, B:T.97, B:T.97, B:E.201 Water bridges: B:M.200 Salt bridges: B:R.33, B:R.94, A:R.51 PO4.6: 9 residues within 4Å: Chain C: G.29, R.33, R.94, I.95, G.96, T.97, E.201 Chain D: R.51 Ligands: 183.8 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.29, C:T.97, C:T.97, C:E.201 Water bridges: C:R.94, C:R.94, D:R.51 Salt bridges: C:R.33, C:R.94, D:R.51 PO4.9: 9 residues within 4Å: Chain C: R.51 Chain D: G.29, R.33, R.94, I.95, G.96, T.97, E.201 Ligands: 183.10 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.29, D:T.97, D:T.97, D:E.201 Water bridges: D:D.30, D:R.94, D:R.94, C:R.51 Salt bridges: D:R.33, D:R.94, C:R.51 PO4.11: 10 residues within 4Å: Chain E: G.29, D.30, R.33, R.94, I.95, G.96, T.97, E.201 Chain F: R.51 Ligands: 183.13 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.29, E:D.30, E:T.97, E:T.97, E:E.201 Water bridges: E:R.94, E:R.94 Salt bridges: E:R.33, E:R.94, F:R.51 PO4.14: 9 residues within 4Å: Chain E: R.51 Chain F: G.29, R.33, R.94, I.95, G.96, T.97, E.201 Ligands: 183.15 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.29, F:T.97, F:T.97, F:E.201 Water bridges: F:R.94, F:E.199 Salt bridges: F:R.33, F:R.94, E:R.51

3 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: E.52, I.72, S.76 Chain B: E.52, I.72, S.76 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:I.72, B:S.76, A:I.72 K.7: 6 residues within 4Å: Chain C: E.52, I.72, S.76 Chain D: E.52, I.72, S.76 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Metal complexes: D:E.52, D:I.72, D:S.76, C:E.52, C:I.72 K.12: 6 residues within 4Å: Chain E: E.52, I.72, S.76 Chain F: E.52, I.72, S.76 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.76

6 x 183: 1-((2-HYDROXYETHOXY)METHYL)-5-(3-(BENZYLOXY)BENZYL)PYRIMIDINE-2,4(1H,3H)-DIONE(Non-covalent)

183.3: 16 residues within 4Å: Chain A: I.72, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, I.223, V.224, M.237 Chain B: F.10, H.11 Ligands: PO4.1 17 PLIP interactions: 6 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:F.10, A:F.165, A:I.223, A:I.223, A:V.224 Hydrogen bonds: B:H.11, A:T.97, A:Q.169, A:Q.169, A:R.171, A:R.171 Water bridges: B:R.51, B:R.51, B:R.51, A:R.94 pi-Stacking: B:F.10, A:F.165 183.5: 18 residues within 4Å: Chain A: F.10, H.11, R.51 Chain B: T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, I.223, V.224, E.230, P.232, M.237 Ligands: PO4.4 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:H.11, B:Q.169, B:Q.169, B:R.171, B:R.171 Water bridges: A:R.51, A:R.51 pi-Stacking: A:F.10, B:F.165 Hydrophobic interactions: B:F.165, B:I.223, B:I.223, B:V.224, B:P.232, B:P.232 183.8: 18 residues within 4Å: Chain C: I.72, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, I.223, V.224, E.230, P.232, M.237 Chain D: F.10, H.11 Ligands: PO4.6 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.165, C:I.223, C:I.223, C:V.224, C:P.232, C:P.232 Hydrogen bonds: C:G.99, C:Q.169, C:Q.169, C:R.171, C:R.171, D:H.11 pi-Stacking: C:F.165, D:F.10 Water bridges: D:R.51, D:R.51, D:R.51 183.10: 18 residues within 4Å: Chain C: F.10, H.11 Chain D: I.72, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, I.223, V.224, E.230, P.232, M.237 Ligands: PO4.9 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.165, D:I.223, D:I.223, D:V.224, D:P.232, D:P.232, C:F.10 Hydrogen bonds: D:G.99, D:Q.169, D:Q.169, D:R.171, D:R.171, C:H.11 Water bridges: D:R.94 pi-Stacking: D:F.165, C:F.10 183.13: 16 residues within 4Å: Chain E: I.72, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, I.223, V.224, M.237 Chain F: F.10, H.11 Ligands: PO4.11 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:F.165, E:I.223, E:V.224, F:F.10 Hydrogen bonds: E:T.97, E:G.99, E:Q.169, E:Q.169, E:R.171, E:R.171, F:H.11 pi-Stacking: E:F.165, F:F.10 183.15: 17 residues within 4Å: Chain E: F.10, H.11 Chain F: I.72, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, I.223, V.224, E.230, P.232 Ligands: PO4.14 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:F.165, F:I.223, F:P.232, E:F.10 Hydrogen bonds: F:T.97, F:Q.169, F:Q.169, F:R.171, F:R.171, E:H.11 pi-Stacking: F:F.165, E:F.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bu, W. et al., Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-07-05

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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