- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.91 Å
- Oligo State
- homo-hexamer
- Ligands
- 4 x URA: URACIL(Non-covalent)
- 7 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 7 residues within 4Å:- Chain A: T.93, F.161, E.195, M.196, E.197
- Chain B: H.7
- Ligands: URA.1
10 PLIP interactions:6 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:T.93, A:T.93, A:M.196, A:E.197, B:H.7
- Water bridges: A:R.90, A:T.93, B:R.47, B:R.47, B:R.47
GOL.6: 7 residues within 4Å:- Chain A: H.7
- Chain B: T.93, F.161, E.195, M.196, E.197
- Ligands: URA.5
8 PLIP interactions:3 interactions with chain A, 5 interactions with chain B- Hydrogen bonds: A:H.7, B:T.93, B:M.196, B:E.197
- Water bridges: A:R.47, A:R.47, B:R.90, B:E.197
GOL.9: 6 residues within 4Å:- Chain C: I.68, F.161, M.196, E.197
- Chain D: H.7, R.47
5 PLIP interactions:2 interactions with chain C, 3 interactions with chain D- Hydrogen bonds: C:E.197, D:H.7
- Water bridges: C:R.90, D:R.47, D:R.47
GOL.12: 6 residues within 4Å:- Chain C: H.7
- Chain D: I.68, F.161, E.195, M.196, E.197
4 PLIP interactions:1 interactions with chain D, 3 interactions with chain C- Hydrogen bonds: D:M.196, C:H.7
- Water bridges: C:R.47, C:R.47
GOL.16: 8 residues within 4Å:- Chain E: I.68, T.93, F.161, E.195, M.196, E.197
- Chain F: H.7
- Ligands: URA.15
10 PLIP interactions:6 interactions with chain E, 4 interactions with chain F- Hydrogen bonds: E:T.93, E:M.196, E:E.197, F:H.7
- Water bridges: E:R.90, E:T.93, E:T.93, F:R.47, F:R.47, F:R.47
GOL.19: 6 residues within 4Å:- Chain E: H.7
- Chain F: T.93, E.195, M.196, E.197
- Ligands: URA.18
5 PLIP interactions:4 interactions with chain F, 1 interactions with chain E- Hydrogen bonds: F:M.196, E:H.7
- Water bridges: F:R.90, F:T.93, F:T.93
GOL.20: 5 residues within 4Å:- Chain F: D.132, C.205, A.206, G.209, L.210
9 PLIP interactions:7 interactions with chain F, 2 interactions with chain A- Hydrogen bonds: F:D.132, F:D.132, F:G.209
- Water bridges: F:F.133, F:A.206, F:K.211, F:A.212, A:T.110, A:V.154
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 3 residues within 4Å:- Chain A: Q.31, T.50, Y.52
1 PLIP interactions:1 interactions with chain A- Water bridges: A:T.50
EDO.10: 8 residues within 4Å:- Chain B: T.110, M.152, G.153
- Chain C: V.130, P.131, D.132, F.133
- Ligands: EDO.11
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain C- Hydrogen bonds: B:M.152, C:P.131, C:F.133
EDO.11: 5 residues within 4Å:- Chain C: D.132, A.206, G.209, L.210
- Ligands: EDO.10
2 PLIP interactions:2 interactions with chain C- Water bridges: C:D.132, C:G.209
EDO.17: 4 residues within 4Å:- Chain E: H.7, H.46, R.47
- Chain F: D.26
4 PLIP interactions:3 interactions with chain E, 1 interactions with chain F- Hydrogen bonds: E:H.7
- Water bridges: E:H.46, E:R.47, F:D.26
- 3 x EOH: ETHANOL(Non-functional Binders)
EOH.4: 3 residues within 4Å:- Chain A: D.134, K.250, M.251
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:D.134
- Water bridges: A:K.250
EOH.13: 2 residues within 4Å:- Chain D: D.169, T.170
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:T.170
EOH.21: 3 residues within 4Å:- Chain E: F.6
- Chain F: F.161, R.167
2 PLIP interactions:1 interactions with chain E, 1 interactions with chain F- Hydrophobic interactions: E:F.6
- Hydrogen bonds: F:D.169
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 3 x NA: SODIUM ION(Non-functional Binders)
NA.8: 6 residues within 4Å:- Chain A: E.48, I.68, S.72
- Chain B: E.48, I.68, S.72
7 PLIP interactions:3 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:E.48, B:I.68, B:S.72, A:I.68, A:S.72, A:S.72
- Water bridges: A:S.72
NA.14: 6 residues within 4Å:- Chain C: E.48, I.68, S.72
- Chain D: E.48, I.68, S.72
6 PLIP interactions:4 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:E.48, C:I.68, C:S.72, D:I.68, D:S.72
- Water bridges: C:S.72
NA.22: 6 residues within 4Å:- Chain E: E.48, I.68, S.72
- Chain F: E.48, I.68, S.72
8 PLIP interactions:4 interactions with chain E, 4 interactions with chain F- Hydrogen bonds: E:E.48, E:I.68, E:S.72, F:E.48, F:E.48, F:I.68, F:S.72
- Water bridges: E:S.72
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Prokofev, I.I. et al., X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases. To Be Published (2016)
- Release Date
- 2015-03-04
- Peptides
- Uridine phosphorylase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.91 Å
- Oligo State
- homo-hexamer
- Ligands
- 4 x URA: URACIL(Non-covalent)
- 7 x GOL: GLYCEROL(Non-functional Binders)
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x EOH: ETHANOL(Non-functional Binders)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 3 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Prokofev, I.I. et al., X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases. To Be Published (2016)
- Release Date
- 2015-03-04
- Peptides
- Uridine phosphorylase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F