MolNFT v1 · #88952 · protein
Crystal structure of the hexameric purine nucleoside phosphorylase from bacillus subtilis in complex with 2-fluoroadenosine
4DAN · Purine nucleoside phosphorylase deod-type: “Crystal structure of the hexameric purine nucleoside phosphorylase from bacillus subtilis in complex with…”. X-ray diffraction, 1 ligand (2FA), 3 pockets (best druggability 0.70). MolNFT…
- PDB
- 4DAN
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- O34925
- Ligands
- 2FA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 229 | 35% helix, 28% strand | O34925 |
| B | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 231 | 35% helix, 28% strand | O34925 |
Ligands and binding sites
- 2FA · 2-(6-amino-2-fluoro-purin-9-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.70 | 0.79 | 60 | 2FA |
| 2 | 429 | 0.68 | 0.80 | 41 | 2FA |
| 3 | 148 | 0.45 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1674 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4DAN · Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis… · the same entry in another collection · chain A against A, TM-score 1.00
- O34925 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (O34925) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O34925
- Elsewhere: RCSB PDB 4DAN · PDBe 4DAN · UniProt O34925
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