- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.87 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
- 6 x FMC: (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol(Non-covalent)
FMC.2: 14 residues within 4Å:- Chain A: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203
- Chain C: H.4, R.43
- Ligands: PO4.1
10 PLIP interactions:8 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: A:R.87, A:S.90, A:M.180, A:E.181, A:S.203, A:S.203, C:H.4, C:R.43
- Water bridges: A:S.90, A:S.90
FMC.5: 15 residues within 4Å:- Chain B: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, I.206
- Chain E: H.4, R.43
- Ligands: PO4.4
7 PLIP interactions:2 interactions with chain E, 5 interactions with chain B- Hydrogen bonds: E:H.4, E:R.43, B:S.90, B:M.180, B:E.181, B:S.203, B:S.203
FMC.9: 13 residues within 4Å:- Chain A: H.4, R.43
- Chain C: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181
- Ligands: PO4.8
5 PLIP interactions:2 interactions with chain A, 3 interactions with chain C- Hydrogen bonds: A:H.4, A:R.43, C:C.91, C:M.180, C:E.181
FMC.11: 14 residues within 4Å:- Chain D: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203
- Chain F: H.4, R.43
- Ligands: PO4.10
10 PLIP interactions:8 interactions with chain D, 2 interactions with chain F- Hydrogen bonds: D:R.87, D:S.90, D:M.180, D:E.181, D:S.203, D:S.203, F:H.4, F:R.43
- Water bridges: D:S.90, D:S.90
FMC.14: 15 residues within 4Å:- Chain B: H.4, R.43
- Chain E: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181, S.203, I.206
- Ligands: PO4.13
7 PLIP interactions:5 interactions with chain E, 2 interactions with chain B- Hydrogen bonds: E:S.90, E:M.180, E:E.181, E:S.203, E:S.203, B:H.4, B:R.43
FMC.18: 13 residues within 4Å:- Chain D: H.4, R.43
- Chain F: M.64, R.87, S.90, C.91, G.92, F.159, V.178, E.179, M.180, E.181
- Ligands: PO4.17
5 PLIP interactions:3 interactions with chain F, 2 interactions with chain D- Hydrogen bonds: F:C.91, F:M.180, F:E.181, D:H.4, D:R.43
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 2 residues within 4Å:- Chain A: N.222, D.223
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:D.223
- Water bridges: A:N.222, A:N.222, A:D.223
- Salt bridges: A:K.226
SO4.6: 4 residues within 4Å:- Chain B: K.99, L.100, H.205, E.210
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:L.100
- Water bridges: B:L.100
- Salt bridges: B:K.99, B:H.205
SO4.7: 3 residues within 4Å:- Chain B: Q.218, T.219, N.222
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Q.218, B:N.222
- Water bridges: B:T.219
SO4.12: 2 residues within 4Å:- Chain D: N.222, D.223
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:D.223
- Water bridges: D:N.222, D:N.222, D:D.223, D:D.223
- Salt bridges: D:K.226
SO4.15: 4 residues within 4Å:- Chain E: K.99, L.100, H.205, E.210
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:L.100
- Water bridges: E:L.100
- Salt bridges: E:K.99, E:H.205
SO4.16: 3 residues within 4Å:- Chain E: Q.218, T.219, N.222
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:Q.218, E:N.222
- Water bridges: E:T.219
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Stefanic, Z. et al., Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis. Sci Rep (2018)
- Release Date
- 2015-07-08
- Peptides
- Purine nucleoside phosphorylase DeoD-type: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
DD
AE
BF
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.87 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
- 6 x FMC: (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol(Non-covalent)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Stefanic, Z. et al., Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis. Sci Rep (2018)
- Release Date
- 2015-07-08
- Peptides
- Purine nucleoside phosphorylase DeoD-type: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
DD
AE
BF
D