MolNFT v1 · #165120 · protein
Purine-nucleoside phosphorylase from thermus thermophilus
6TK9 · Purine nucleoside phosphorylase: “Purine-nucleoside phosphorylase from thermus thermophilus”. X-ray diffraction, 1 ligand (PO4), 15 pockets (best druggability 0.87). MolNFT v1 #165120 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6TK9
- Type
- protein
- Length
- 1,626 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- A0A510IGW9
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 271 | 34% helix, 25% strand | A0A510IGW9 |
Ligands and binding sites
- PO4 · Phosphate 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
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.87 | 0.93 | 89 | empty |
| 2 | 387 | 0.84 | 0.92 | 58 | empty |
| 3 | 129 | 0.80 | 0.97 | 30 | PO4 |
| 4 | 117 | 0.79 | 0.97 | 29 | PO4 |
| 5 | 113 | 0.79 | 0.98 | 28 | PO4 |
Interfaces
13 interfaces between chains.
- D–F · 1239 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1231 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1225 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1202 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1198 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6TK9 · 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
- Every structure of UniProt A0A510IGW9
- Elsewhere: RCSB PDB 6TK9 · PDBe 6TK9 · UniProt A0A510IGW9
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