- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-hexamer
- Ligands
- 21 x GOL: GLYCEROL(Non-functional Binders)
- 3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
TRS.7: 11 residues within 4Å:- Chain A: H.4, R.43
- Chain B: M.64, R.87, T.90, F.159, E.179, M.180, E.181
- Ligands: PO4.8, 05Z.9
6 PLIP interactions:2 interactions with chain A, 4 interactions with chain B- Hydrogen bonds: A:H.4, B:R.87, B:T.90, B:M.180
- Water bridges: A:R.43, B:S.203
TRS.17: 11 residues within 4Å:- Chain C: H.4, R.43
- Chain D: M.64, R.87, T.90, F.159, E.179, M.180, E.181
- Ligands: PO4.18, 05Z.19
6 PLIP interactions:4 interactions with chain D, 2 interactions with chain C- Hydrogen bonds: D:R.87, D:T.90, D:M.180, C:H.4
- Water bridges: D:S.203, C:R.43
TRS.27: 11 residues within 4Å:- Chain E: H.4, R.43
- Chain F: M.64, R.87, T.90, F.159, E.179, M.180, E.181
- Ligands: PO4.28, 05Z.29
7 PLIP interactions:2 interactions with chain E, 5 interactions with chain F- Hydrogen bonds: E:H.4, F:R.87, F:T.90, F:T.90, F:M.180
- Water bridges: E:R.43, F:S.203
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.8: 10 residues within 4Å:- Chain A: R.43
- Chain B: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181
- Ligands: TRS.7
9 PLIP interactions:1 interactions with chain A, 8 interactions with chain B- Salt bridges: A:R.43, B:R.24, B:R.87
- Hydrogen bonds: B:G.20, B:D.21, B:T.90, B:T.90, B:T.90
- Water bridges: B:S.203
PO4.18: 10 residues within 4Å:- Chain C: R.43
- Chain D: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181
- Ligands: TRS.17
9 PLIP interactions:8 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:G.20, D:D.21, D:T.90, D:T.90, D:T.90
- Water bridges: D:S.203
- Salt bridges: D:R.24, D:R.87, C:R.43
PO4.28: 10 residues within 4Å:- Chain E: R.43
- Chain F: C.19, G.20, D.21, R.24, R.87, G.89, T.90, E.181
- Ligands: TRS.27
9 PLIP interactions:8 interactions with chain F, 1 interactions with chain E- Hydrogen bonds: F:G.20, F:D.21, F:T.90, F:T.90, F:T.90
- Water bridges: F:S.203
- Salt bridges: F:R.24, F:R.87, E:R.43
- 3 x 05Z: 6-benzylthio-2-chloropurine(Non-covalent)
05Z.9: 13 residues within 4Å:- Chain B: T.90, C.91, G.92, F.158, F.159, Y.160, I.178, E.179, M.180, S.203, D.204
- Ligands: TRS.7, GOL.10
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:F.159, B:Y.160
- Hydrogen bonds: B:D.204, B:D.204
- Halogen bonds: B:F.158
05Z.19: 13 residues within 4Å:- Chain D: T.90, C.91, G.92, F.158, F.159, Y.160, I.178, E.179, M.180, S.203, D.204
- Ligands: TRS.17, GOL.20
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:F.159, D:Y.160
- Hydrogen bonds: D:D.204, D:D.204
- Halogen bonds: D:F.158
05Z.29: 13 residues within 4Å:- Chain F: T.90, C.91, G.92, F.158, F.159, Y.160, I.178, E.179, M.180, S.203, D.204
- Ligands: TRS.27, GOL.30
6 PLIP interactions:6 interactions with chain F- Hydrophobic interactions: F:F.159, F:Y.160
- Hydrogen bonds: F:T.90, F:D.204, F:D.204
- Halogen bonds: F:F.158
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Narczyk, M. et al., Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium. J Enzyme Inhib Med Chem (2022)
- Release Date
- 2022-05-04
- Peptides
- Purine nucleoside phosphorylase DeoD-type: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-hexamer
- Ligands
- 21 x GOL: GLYCEROL(Non-functional Binders)
- 3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 3 x PO4: PHOSPHATE ION(Non-functional Binders)
- 3 x 05Z: 6-benzylthio-2-chloropurine(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Narczyk, M. et al., Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium. J Enzyme Inhib Med Chem (2022)
- Release Date
- 2022-05-04
- Peptides
- Purine nucleoside phosphorylase DeoD-type: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B