- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.17 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x 6MU: 6-methylpyrimidine-2,4-diol(Non-covalent)
6MU.3: 12 residues within 4Å:- Chain A: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:I.219, A:I.220
- Hydrogen bonds: A:Q.165, A:Q.165, A:R.167, A:R.167, A:F.194
- Water bridges: A:T.94, A:G.95, A:G.95, A:M.196
6MU.12: 15 residues within 4Å:- Chain A: F.6
- Chain B: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222, P.228
- Ligands: TRS.17
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:I.219
- Hydrogen bonds: B:Q.165, B:Q.165, B:R.167, B:R.167, B:F.194
6MU.23: 15 residues within 4Å:- Chain C: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222, P.228
- Chain D: F.6
- Ligands: TRS.28
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:I.219
- Hydrogen bonds: C:Q.165, C:Q.165, C:R.167, C:R.167, C:F.194
6MU.33: 13 residues within 4Å:- Chain D: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222
- Ligands: GOL.31
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:Q.165, D:Q.165, D:R.167, D:R.167, D:F.194
6MU.40: 13 residues within 4Å:- Chain E: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222
- Ligands: TRS.44
5 PLIP interactions:5 interactions with chain E- Hydrophobic interactions: E:I.219
- Hydrogen bonds: E:Q.165, E:Q.165, E:R.167, E:R.167
6MU.49: 13 residues within 4Å:- Chain F: T.93, T.94, G.95, F.161, Q.165, R.167, F.194, E.195, M.196, I.219, I.220, R.222
- Ligands: TRS.43
7 PLIP interactions:7 interactions with chain F- Hydrophobic interactions: F:I.219
- Hydrogen bonds: F:Q.165, F:Q.165, F:R.167, F:R.167, F:F.194
- Water bridges: F:M.196
- 16 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.4: 1 residues within 4Å:- Chain A: Q.180
No protein-ligand interaction detected (PLIP)MG.5: 1 residues within 4Å:- Chain A: A.206
No protein-ligand interaction detected (PLIP)MG.13: 2 residues within 4Å:- Chain B: R.177, Q.180
No protein-ligand interaction detected (PLIP)MG.14: 1 residues within 4Å:- Chain B: A.206
No protein-ligand interaction detected (PLIP)MG.15: 1 residues within 4Å:- Chain B: F.171
No protein-ligand interaction detected (PLIP)MG.24: 2 residues within 4Å:- Chain C: R.177, Q.180
No protein-ligand interaction detected (PLIP)MG.25: 1 residues within 4Å:- Chain C: K.250
No protein-ligand interaction detected (PLIP)MG.26: 1 residues within 4Å:- Chain C: A.206
No protein-ligand interaction detected (PLIP)MG.34: 2 residues within 4Å:- Chain D: R.177, Q.180
No protein-ligand interaction detected (PLIP)MG.35: 2 residues within 4Å:- Chain D: G.9, H.46
5 PLIP interactions:1 interactions with chain D, 4 Ligand-Water interactions- Metal complexes: D:H.46, H2O.51, H2O.56, H2O.61, H2O.62
MG.36: 1 residues within 4Å:- Chain D: A.206
No protein-ligand interaction detected (PLIP)MG.41: 1 residues within 4Å:- Chain E: Q.180
No protein-ligand interaction detected (PLIP)MG.46: 1 residues within 4Å:- Chain E: A.206
No protein-ligand interaction detected (PLIP)MG.50: 2 residues within 4Å:- Chain F: R.177, Q.180
No protein-ligand interaction detected (PLIP)MG.51: 3 residues within 4Å:- Chain F: N.102, Q.224
- Ligands: MG.52
No protein-ligand interaction detected (PLIP)MG.52: 3 residues within 4Å:- Chain F: H.100, N.102
- Ligands: MG.51
No protein-ligand interaction detected (PLIP)- 4 x NA: SODIUM ION(Non-functional Binders)
NA.6: 8 residues within 4Å:- Chain A: E.48, G.67, I.68, S.72
- Chain B: E.48, G.67, I.68, S.72
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:I.68, B:S.72, B:S.72, A:I.68, A:S.72
- Water bridges: A:S.72
NA.16: 8 residues within 4Å:- Chain B: P.163, R.167, Y.168, T.170, T.172, G.173, R.174, V.175
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:T.170, B:T.170, B:R.174
- Water bridges: B:T.172
NA.27: 8 residues within 4Å:- Chain C: E.48, G.67, I.68, S.72
- Chain D: E.48, G.67, I.68, S.72
7 PLIP interactions:4 interactions with chain C, 3 interactions with chain D- Hydrogen bonds: C:E.48, C:I.68, C:S.72, D:E.48, D:I.68, D:S.72
- Water bridges: C:S.72
NA.42: 8 residues within 4Å:- Chain E: E.48, G.67, I.68, S.72
- Chain F: E.48, G.67, I.68, S.72
8 PLIP interactions:5 interactions with chain F, 3 interactions with chain E- Hydrogen bonds: F:E.48, F:E.48, F:I.68, F:S.72, E:E.48, E:I.68, E:S.72
- Water bridges: F:S.72
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 3 residues within 4Å:- Chain A: M.125
- Chain F: M.125, E.126
3 PLIP interactions:1 interactions with chain F, 2 interactions with chain A- Hydrogen bonds: F:E.126
- Water bridges: A:E.126, A:E.126
EDO.18: 7 residues within 4Å:- Chain B: P.99, V.101, N.102, V.103, N.221, Q.224
- Ligands: CL.11
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:P.99, B:V.103
- Water bridges: B:N.102
EDO.37: 4 residues within 4Å:- Chain D: M.125, E.126
- Chain E: M.125, E.126
2 PLIP interactions:1 interactions with chain E, 1 interactions with chain D- Hydrogen bonds: E:E.126, D:E.126
EDO.53: 5 residues within 4Å:- Chain E: K.3, Q.82
- Chain F: D.169, T.170, F.171
2 PLIP interactions:1 interactions with chain F, 1 interactions with chain E- Hydrogen bonds: F:D.169, E:K.3
- 7 x EOH: ETHANOL(Non-functional Binders)
EOH.8: 4 residues within 4Å:- Chain A: R.178
- Chain B: L.120, P.124, M.125
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.178
EOH.19: 4 residues within 4Å:- Chain A: L.120, P.124, M.125
- Chain B: R.178
1 PLIP interactions:1 interactions with chain A- Water bridges: A:A.123
EOH.29: 6 residues within 4Å:- Chain C: P.99, V.101, N.102, V.103, N.221, Q.224
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:N.221
- Hydrogen bonds: C:N.102, C:V.103
EOH.30: 4 residues within 4Å:- Chain C: R.178
- Chain D: L.120, P.124, M.125
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.178
EOH.38: 4 residues within 4Å:- Chain C: L.120, P.124, M.125
- Chain D: R.178
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:R.178
EOH.45: 4 residues within 4Å:- Chain E: R.178
- Chain F: L.120, P.124, M.125
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:R.178
EOH.54: 4 residues within 4Å:- Chain E: L.120, P.124, M.125
- Chain F: R.178
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:R.178
- 4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
TRS.17: 16 residues within 4Å:- Chain A: F.6, H.7, R.47, I.75
- Chain B: G.25, G.67, I.68, G.69, R.90, T.93, F.161, Q.165, E.195, M.196, E.197
- Ligands: 6MU.12
12 PLIP interactions:5 interactions with chain A, 7 interactions with chain B- Hydrogen bonds: A:H.7, A:R.47, B:T.93, B:M.196
- Water bridges: A:R.47, A:R.47, A:R.47, B:R.90, B:R.90, B:R.90, B:E.197, B:E.197
TRS.28: 16 residues within 4Å:- Chain C: G.25, G.67, I.68, G.69, R.90, T.93, F.161, Q.165, E.195, M.196, E.197
- Chain D: F.6, H.7, R.47, I.75
- Ligands: 6MU.23
11 PLIP interactions:8 interactions with chain C, 3 interactions with chain D- Hydrogen bonds: C:T.93, C:M.196, D:H.7, D:R.47, D:R.47
- Water bridges: C:R.90, C:R.90, C:T.93, C:E.197, C:E.197, C:E.197
TRS.43: 15 residues within 4Å:- Chain E: H.7, R.47, I.75
- Chain F: G.25, G.67, I.68, G.69, R.90, T.93, T.94, F.161, E.195, M.196, E.197
- Ligands: 6MU.49
9 PLIP interactions:5 interactions with chain F, 4 interactions with chain E- Hydrogen bonds: F:T.93, F:E.197, E:H.7, E:R.47
- Water bridges: F:R.90, F:T.93, F:T.93, E:R.47, E:R.47
TRS.44: 15 residues within 4Å:- Chain E: G.25, G.67, I.68, G.69, R.90, T.93, F.161, Q.165, E.195, M.196, E.197
- Chain F: H.7, R.47, I.75
- Ligands: 6MU.40
10 PLIP interactions:7 interactions with chain E, 3 interactions with chain F- Hydrogen bonds: E:T.93, E:M.196, F:H.7, F:R.47, F:R.47
- Water bridges: E:R.90, E:R.90, E:T.93, E:E.197, E:E.197
- 1 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Prokofev, I.I. et al., Crystallization and preliminary X-ray study of Vibrio cholerae uridine phosphorylase in complex with 6-methyluracil. Acta Crystallogr.,Sect.F (2014)
- Release Date
- 2014-05-07
- 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 1.17 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x 6MU: 6-methylpyrimidine-2,4-diol(Non-covalent)
- 16 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 7 x EOH: ETHANOL(Non-functional Binders)
- 4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Prokofev, I.I. et al., Crystallization and preliminary X-ray study of Vibrio cholerae uridine phosphorylase in complex with 6-methyluracil. Acta Crystallogr.,Sect.F (2014)
- Release Date
- 2014-05-07
- Peptides
- Uridine phosphorylase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F