SMTL ID : 1tgv.1

Structure of E. coli Uridine Phosphorylase complexed with 5-Fluorouridine and sulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 10 residues within 4Å: Chain A: G.29, D.30, R.33, R.94, I.95, G.96, T.97, E.201 Chain B: R.51 Ligands: 5UD.3 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Salt bridges: B:R.51, A:R.33, A:R.94 Hydrogen bonds: A:G.29, A:D.30, A:T.97 SO4.4: 10 residues within 4Å: Chain A: R.51 Chain B: G.29, D.30, R.33, R.94, I.95, G.96, T.97, E.201 Ligands: 5UD.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.29, B:D.30, B:T.97 Salt bridges: B:R.33, B:R.94, A:R.51 SO4.6: 10 residues within 4Å: Chain C: G.29, D.30, R.33, R.94, I.95, G.96, T.97, E.201 Chain D: R.51 Ligands: 5UD.8 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.29, C:D.30, C:T.97 Salt bridges: C:R.33, C:R.94, D:R.51 SO4.9: 10 residues within 4Å: Chain C: R.51 Chain D: G.29, D.30, R.33, R.94, I.95, G.96, T.97, E.201 Ligands: 5UD.10 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.29, D:D.30, D:T.97 Salt bridges: D:R.33, D:R.94, C:R.51 SO4.11: 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: 5UD.13 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.29, E:D.30, E:T.97 Salt bridges: E:R.33, E:R.94, F:R.51 SO4.14: 10 residues within 4Å: Chain E: R.51 Chain F: G.29, D.30, R.33, R.94, I.95, G.96, T.97, E.201 Ligands: 5UD.15 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.29, F:D.30, F:T.97 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 No protein-ligand interaction detected (PLIP) K.7: 6 residues within 4Å: Chain C: E.52, I.72, S.76 Chain D: E.52, I.72, S.76 No protein-ligand interaction detected (PLIP) K.12: 6 residues within 4Å: Chain E: E.52, I.72, S.76 Chain F: E.52, I.72, S.76 No protein-ligand interaction detected (PLIP)

6 x 5UD: 5-FLUOROURIDINE(Non-covalent)

5UD.3: 17 residues within 4Å: Chain A: I.72, R.94, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, E.201, I.223, V.224 Chain B: F.10, H.11 Ligands: SO4.1 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.94, A:T.97, A:Q.169, A:Q.169, A:R.171, A:R.171, A:M.200, A:E.201, B:H.11 Water bridges: B:R.51, B:R.51 5UD.5: 17 residues within 4Å: Chain A: F.10, H.11 Chain B: I.72, R.94, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, E.201, I.223, V.224 Ligands: SO4.4 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.94, B:T.97, B:Q.169, B:Q.169, B:R.171, B:R.171, B:E.199, B:M.200, B:E.201, A:H.11 Water bridges: A:R.51, A:R.51 5UD.8: 17 residues within 4Å: Chain C: I.72, R.94, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, E.201, I.223, V.224 Chain D: F.10, H.11 Ligands: SO4.6 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:H.11, C:R.94, C:T.97, C:Q.169, C:Q.169, C:R.171, C:R.171, C:M.200, C:E.201 Water bridges: D:R.51, D:R.51 5UD.10: 17 residues within 4Å: Chain C: F.10, H.11 Chain D: I.72, R.94, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, E.201, I.223, V.224 Ligands: SO4.9 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.94, D:T.97, D:Q.169, D:Q.169, D:R.171, D:R.171, D:E.199, D:M.200, D:E.201, C:H.11 Water bridges: C:R.51, C:R.51 5UD.13: 17 residues within 4Å: Chain E: I.72, R.94, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, E.201, I.223, V.224 Chain F: F.10, H.11 Ligands: SO4.11 11 PLIP interactions: 3 interactions with chain F, 8 interactions with chain E Hydrogen bonds: F:H.11, E:R.94, E:T.97, E:Q.169, E:Q.169, E:R.171, E:R.171, E:M.200, E:E.201 Water bridges: F:R.51, F:R.51 5UD.15: 17 residues within 4Å: Chain E: F.10, H.11 Chain F: I.72, R.94, T.97, T.98, G.99, F.165, Q.169, R.171, Y.198, E.199, M.200, E.201, I.223, V.224 Ligands: SO4.14 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:R.94, F:T.97, F:Q.169, F:Q.169, F:R.171, F:R.171, F:E.199, F:M.200, F:E.201, E:H.11 Water bridges: E:R.51, E:R.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bu, W. et al., Structures of E. coli Uridine Phosphorylase. To be Published (2004)

Release Date

2005-06-14

Peptides

uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

uridine phosphorylase

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