Research workbench
Crystal structure of the purine nucleoside phosphorylase from schistosoma mansoni in complex with acetate
Analyse Crystal structure of the purine nucleoside phosphorylase from schistosoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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