MolNFT v1 · #62248 · protein
Crystal structure of purine nucleoside phosphorylase from schistosoma mansoni in complex with 6-chloroguanine
3E9Z · Purine-nucleoside phosphorylase: “Crystal structure of purine nucleoside phosphorylase from schistosoma mansoni in complex with 6-chloroguanine”. X-ray diffraction, 2 ligands (6GU, SO4), 6 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 3E9Z
- Type
- protein
- Length
- 833 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
- 6GU, SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 280 | 36% helix, 24% strand | Q9BMI9 |
| B | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 270 | 34% helix, 25% strand | Q9BMI9 |
| C | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 283 | 37% helix, 24% strand | Q9BMI9 |
Ligands and binding sites
- 6GU · 6-chloroguanine · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.74 | 0.99 | 20 | DMS |
| 2 | 403 | 0.67 | 0.80 | 44 | 6GU, SO4 |
| 3 | 281 | 0.63 | 0.81 | 38 | SO4, 6GU |
| 4 | 83 | 0.49 | 0.82 | 20 | empty |
| 5 | 217 | 0.46 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1319 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1288 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1152 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3E9Z · 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 3E9Z · PDBe 3E9Z · UniProt Q9BMI9
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