- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.69 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x FMC: (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol(Non-covalent)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.2: 9 residues within 4Å:- Chain A: C.19, G.20, D.21, R.87, G.89, T.90, E.181
- Chain D: R.43
- Ligands: FMC.1
7 PLIP interactions:6 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:G.20, A:D.21, A:T.90, A:T.90
- Water bridges: A:E.179
- Salt bridges: A:R.87, D:R.43
PO4.10: 10 residues within 4Å:- Chain C: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181
- Chain F: R.43
- Ligands: FMC.11
6 PLIP interactions:5 interactions with chain C, 1 interactions with chain F- Hydrogen bonds: C:G.20, C:D.21, C:T.90
- Salt bridges: C:R.24, C:R.87, F:R.43
PO4.17: 10 residues within 4Å:- Chain B: R.43
- Chain E: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181
- Ligands: FMC.18
7 PLIP interactions:1 interactions with chain B, 6 interactions with chain E- Salt bridges: B:R.43, E:R.24, E:R.87
- Hydrogen bonds: E:G.20, E:D.21, E:T.90
- Water bridges: E:S.203
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 6 residues within 4Å:- Chain A: Y.13, D.35, K.37, S.49, G.50, K.51
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.13, A:S.49
EDO.4: 4 residues within 4Å:- Chain A: K.78, E.191
- Chain D: Y.160, F.162
6 PLIP interactions:4 interactions with chain A, 2 interactions with chain D- Hydrogen bonds: A:K.78, A:E.191
- Water bridges: A:T.74, A:E.191, D:S.161, D:S.161
EDO.5: 5 residues within 4Å:- Chain A: N.6, E.38, I.39, T.40, N.41
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.38, A:T.40
- Water bridges: A:N.6
EDO.6: 3 residues within 4Å:- Chain A: K.30, A.36, F.48
1 PLIP interactions:1 interactions with chain A- Water bridges: A:E.38
EDO.7: 5 residues within 4Å:- Chain A: R.117, V.118, L.121, N.122
- Chain D: E.163
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain D- Water bridges: A:L.121
- Hydrogen bonds: D:E.163
EDO.9: 4 residues within 4Å:- Chain B: P.14, Q.15, R.55, K.83
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Q.15, B:R.55
- Water bridges: B:E.84, B:E.84
EDO.12: 6 residues within 4Å:- Chain C: T.74, K.78, E.191, L.192
- Chain F: Y.160, F.162
5 PLIP interactions:2 interactions with chain F, 3 interactions with chain C- Water bridges: F:Y.160, F:S.161, C:E.191, C:E.191
- Hydrogen bonds: C:K.78
EDO.14: 6 residues within 4Å:- Chain D: C.19, R.24, I.88, T.90, F.221, M.224
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:R.24
EDO.15: 4 residues within 4Å:- Chain B: V.150
- Chain D: D.130, F.131, E.132
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain D- Hydrogen bonds: B:V.150, D:D.130, D:F.131, D:E.132
- Water bridges: B:N.174
EDO.16: 3 residues within 4Å:- Chain D: P.96, K.97, V.98
No protein-ligand interaction detected (PLIP)EDO.19: 5 residues within 4Å:- Chain C: R.119
- Chain E: L.169, K.172, Y.173
- Chain F: F.162
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Y.173
- Water bridges: E:K.172
EDO.21: 4 residues within 4Å:- Chain F: G.10, D.11, Y.13, S.49
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:G.10, F:S.49
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Narczyk, M. et al., Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features. FEBS J. (2018)
- Release Date
- 2018-02-14
- Peptides
- Purine nucleoside phosphorylase DeoD-type: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.69 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x FMC: (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol(Non-covalent)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Narczyk, M. et al., Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features. FEBS J. (2018)
- Release Date
- 2018-02-14
- Peptides
- Purine nucleoside phosphorylase DeoD-type: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F