MolNFT v1 · #16934 · protein
Purine nucleoside phosphorylase from thermus thermophilus
1ODI: “Purine nucleoside phosphorylase from thermus thermophilus”. X-ray diffraction, 2 ligands (ADN, SO4), 17 pockets (best druggability 0.78). MolNFT v1 #16934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ODI
- Type
- protein
- Length
- 1,404 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.28
- Ligands
- ADN, SO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Purine nucleoside phosphorylase (EC 2.4.2.28) | protein | 234 | 38% helix, 28% strand | — |
Ligands and binding sites
- ADN · Adenosine · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.78 | 0.80 | 99 | empty |
| 2 | 60 | 0.71 | 0.97 | 20 | empty |
| 3 | 60 | 0.71 | 0.97 | 20 | empty |
| 4 | 640 | 0.71 | 0.79 | 56 | empty |
| 5 | 340 | 0.70 | 0.83 | 46 | SO4, ADN |
Interfaces
6 interfaces between chains.
- A–B · 1720 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1695 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1659 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1413 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1376 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1ODI · Purine nucleoside phosphorylase from Thermus Thermophilus · 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
- Elsewhere: RCSB PDB 1ODI · PDBe 1ODI
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