- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.34 Å
- Oligo State
- homo-hexamer
- Ligands
- 3 x NA: SODIUM ION(Non-functional Binders)
- 6 x BJE: 2,2'-Anhydro-(1-beta-D-ribofuranosyl)uracil(Non-covalent)
BJE.2: 12 residues within 4Å:- Chain A: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197
- Chain B: H.7, R.47
13 PLIP interactions:9 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:G.95, A:Q.165, A:E.197, B:H.7, B:R.47
- Water bridges: A:R.90, A:T.93, A:T.93, A:T.93, A:R.167, A:R.167, B:R.47, B:R.47
BJE.3: 12 residues within 4Å:- Chain A: H.7, R.47
- Chain B: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197
13 PLIP interactions:9 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:T.93, B:G.95, B:Q.165, B:E.197, A:H.7, A:R.47
- Water bridges: B:R.90, B:T.93, B:T.93, B:R.167, B:R.167, A:R.47, A:R.47
BJE.7: 12 residues within 4Å:- Chain C: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197
- Chain D: H.7, R.47
12 PLIP interactions:4 interactions with chain D, 8 interactions with chain C- Hydrogen bonds: D:H.7, D:R.47, C:G.95, C:Q.165, C:M.196, C:E.197
- Water bridges: D:R.47, D:R.47, C:R.90, C:R.90, C:T.93, C:R.167
BJE.9: 12 residues within 4Å:- Chain C: H.7, R.47
- Chain D: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197
14 PLIP interactions:10 interactions with chain D, 4 interactions with chain C- Hydrogen bonds: D:T.93, D:G.95, D:Q.165, D:M.196, D:E.197, C:H.7, C:R.47
- Water bridges: D:R.90, D:T.93, D:T.93, D:R.167, D:R.167, C:R.47, C:R.47
BJE.14: 12 residues within 4Å:- Chain E: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197
- Chain F: H.7, R.47
12 PLIP interactions:8 interactions with chain E, 4 interactions with chain F- Hydrogen bonds: E:G.95, E:Q.165, E:E.197, F:H.7, F:R.47
- Water bridges: E:R.90, E:T.93, E:T.93, E:R.167, E:R.167, F:R.47, F:R.47
BJE.16: 12 residues within 4Å:- Chain E: H.7, R.47
- Chain F: I.68, T.93, T.94, G.95, F.161, Q.165, F.194, E.195, M.196, E.197
14 PLIP interactions:10 interactions with chain F, 4 interactions with chain E- Hydrogen bonds: F:T.93, F:G.95, F:Q.165, F:M.196, F:E.197, E:H.7, E:R.47
- Water bridges: F:R.90, F:R.90, F:T.93, F:R.167, F:R.167, E:R.47, E:R.47
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 7 residues within 4Å:- Chain B: L.115, R.178, F.179, E.185, W.186
- Chain C: P.124, E.126
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:R.178, B:E.185, C:E.126
- Water bridges: B:R.178
GOL.5: 7 residues within 4Å:- Chain B: T.4, V.5, F.6, H.7, L.8, G.9, H.46
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:T.4, B:G.9, B:H.46
GOL.10: 6 residues within 4Å:- Chain D: L.115, R.178, F.179, E.185
- Chain E: E.126
- Chain F: R.177
6 PLIP interactions:2 interactions with chain E, 4 interactions with chain D- Hydrogen bonds: E:E.126, D:R.178, D:R.178, D:E.185
- Water bridges: E:E.126, D:R.178
GOL.11: 4 residues within 4Å:- Chain D: P.99, H.100, N.102, Q.224
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:P.99, D:N.102, D:Q.224
- Water bridges: D:N.102
GOL.12: 4 residues within 4Å:- Chain C: Q.82
- Chain D: D.169, T.170, F.171
5 PLIP interactions:3 interactions with chain C, 2 interactions with chain D- Water bridges: C:A.81, C:Q.82, C:Q.82, D:T.170
- Hydrogen bonds: D:D.169
GOL.18: 6 residues within 4Å:- Chain A: E.126
- Chain B: R.177
- Chain F: L.115, R.178, F.179, E.185
4 PLIP interactions:1 interactions with chain B, 2 interactions with chain F, 1 interactions with chain A- Water bridges: B:R.177
- Hydrogen bonds: F:R.178, F:E.185, A:E.126
GOL.19: 3 residues within 4Å:- Chain F: K.184, Q.187, D.188
5 PLIP interactions:5 interactions with chain F- Hydrogen bonds: F:K.184, F:Q.187
- Water bridges: F:Q.187, F:Q.187, F:D.188
GOL.20: 4 residues within 4Å:- Chain E: D.169, T.170, F.171
- Chain F: Q.82
3 PLIP interactions:2 interactions with chain E, 1 interactions with chain F- Hydrogen bonds: E:D.169, F:Q.82
- Water bridges: E:T.170
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x MG: MAGNESIUM ION(Non-functional Binders)
- 1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Eistrikh-Geller, P.A. et al., X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-Anhydrouridine. Crystallography Reports (2020)
- Release Date
- 2020-05-13
- 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 1.34 Å
- Oligo State
- homo-hexamer
- Ligands
- 3 x NA: SODIUM ION(Non-functional Binders)
- 6 x BJE: 2,2'-Anhydro-(1-beta-D-ribofuranosyl)uracil(Non-covalent)
- 8 x GOL: GLYCEROL(Non-functional Binders)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x MG: MAGNESIUM ION(Non-functional Binders)
- 1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Eistrikh-Geller, P.A. et al., X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-Anhydrouridine. Crystallography Reports (2020)
- Release Date
- 2020-05-13
- Peptides
- Uridine phosphorylase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F