Research workbench
Crystal structure of the hexameric purine nucleoside phosphorylase from bacillus subtilis at pH 4.2
Analyse Crystal structure of the hexameric purine nucleoside phosphorylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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