MolNFT v1 · #22686 · protein
Crystal structure of the purine nucleoside phosphorylase from schistosoma mansoni in complex with acetate
1TD1 · Purine-nucleoside phosphorylase: “Crystal structure of the purine nucleoside phosphorylase from schistosoma mansoni in complex with acetate”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #22686 on GenesisL1: 3D…
- PDB
- 1TD1
- Type
- protein
- Length
- 839 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
- Pockets
- 8 · best druggability 0.73
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 | 282 | 37% helix, 23% strand | Q9BMI9 |
| B | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 272 | 33% helix, 25% strand | Q9BMI9 |
| C | Purine-nucleoside phosphorylase (EC 2.4.2.1) | protein | 285 | 35% helix, 25% strand | Q9BMI9 |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.73 | 0.98 | 21 | empty |
| 2 | 424 | 0.65 | 0.79 | 44 | ACT |
| 3 | 306 | 0.61 | 0.79 | 38 | ACT |
| 4 | 294 | 0.52 | 0.74 | 41 | empty |
| 5 | 218 | 0.50 | 0.75 | 39 | ACT |
Interfaces
3 interfaces between chains.
- A–C · 1268 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1238 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1149 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1TD1 · Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in… · 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 1TD1 · PDBe 1TD1 · UniProt Q9BMI9
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