MolNFT v1 · #16935 · protein
Purine nucleoside phosphorylase from thermus thermophilus
1ODJ: “Purine nucleoside phosphorylase from thermus thermophilus”. X-ray diffraction, 2 ligands (GMP, SO4), 16 pockets (best druggability 0.82). MolNFT v1 #16935 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ODJ
- 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
- GMP, SO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 29% 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 | 37% helix, 29% strand | — |
Ligands and binding sites
- GMP · Guanosine · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.82 | 0.85 | 123 | empty |
| 2 | 424 | 0.73 | 0.83 | 49 | SO4, GMP |
| 3 | 344 | 0.72 | 0.84 | 40 | SO4, GMP |
| 4 | 402 | 0.72 | 0.83 | 51 | SO4, GMP |
| 5 | 371 | 0.71 | 0.83 | 45 | SO4, GMP |
Interfaces
6 interfaces between chains.
- A–B · 1682 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1643 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1628 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1392 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1386 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1ODJ · 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 1ODJ · PDBe 1ODJ
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