MolNFT v1 · #88894 · protein
Crystal structure of the hexameric purine nucleoside phosphorylase from bacillus subtilis at pH 4.2
4D8V · Purine nucleoside phosphorylase deod-type: “Crystal structure of the hexameric purine nucleoside phosphorylase from bacillus subtilis at pH 4.2”. X-ray diffraction, 2 ligands (ADE, SO4), 5 pockets (best druggability 0.66). MolNFT v1…
- PDB
- 4D8V
- Type
- protein
- Length
- 462 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
- ADE, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 231 | 34% helix, 28% strand | O34925 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.66 | 0.80 | 46 | SO4, ADE |
| 2 | 286 | 0.64 | 0.81 | 40 | SO4, ADE |
| 3 | 165 | 0.46 | 0.76 | 23 | empty |
| 4 | 145 | 0.45 | 0.77 | 26 | empty |
| 5 | 67 | 0.41 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1676 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4D8V · 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 B 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 4D8V · PDBe 4D8V · UniProt O34925
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