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Crystal structure of schistosoma purine nucleoside phosphorylase in complex with hypoxanthine
Analyse Crystal structure of schistosoma purine nucleoside phosphorylase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FNQ
- Type
- protein
- Length
- 833 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Schistosoma mansoni
- Molecule
- Purine-nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- Q9BMI9
- Ligands
- HPA, SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.85 · 3 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 280 | 37% helix, 24% strand | Q9BMI9 |
| B | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 271 | 36% helix, 25% strand | Q9BMI9 |
| C | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 282 | 38% helix, 25% strand | Q9BMI9 |
Ligands and binding sites
- HPA · Hypoxanthine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.76 | 0.99 | 18 | SO4 |
| 2 | 412 | 0.68 | 0.81 | 44 | HPA, SO4 |
| 3 | 201 | 0.63 | 0.84 | 29 | HPA |
| 4 | 319 | 0.62 | 0.79 | 41 | HPA, SO4 |
| 5 | 210 | 0.44 | 0.73 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1273 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1265 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1260 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3FNQ · Crystal structure of schistosoma purine nucleoside phosphorylase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9BMI9
- Elsewhere: RCSB PDB 3FNQ · PDBe 3FNQ · UniProt Q9BMI9
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