Research workbench
Crystal structure of purine nucleoside phosphorylase from schistosoma mansoni in complex with adenine
Analyse Crystal structure of purine nucleoside phosphorylase from schistosoma mansoni… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E9R
- Type
- protein
- Length
- 842 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine-nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- Q9BMI9
- Ligands
- ADE, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 285 | 36% helix, 25% strand | Q9BMI9 |
| B | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 273 | 33% helix, 24% strand | Q9BMI9 |
| C | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 284 | 36% helix, 24% strand | Q9BMI9 |
Ligands and binding sites
- ADE · Adenine · ligand · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.76 | 0.98 | 21 | SO4 |
| 2 | 409 | 0.67 | 0.80 | 45 | SO4, ACT |
| 3 | 404 | 0.66 | 0.79 | 42 | SO4, ACT |
| 4 | 248 | 0.56 | 0.78 | 42 | ADE, SO4 |
| 5 | 212 | 0.43 | 0.72 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1312 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1287 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1110 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3E9R · Crystal structure of purine nucleoside phosphorylase from Schistosoma mansoni in complex… · 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 3E9R · PDBe 3E9R · UniProt Q9BMI9
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