MolNFT v1 · #88956 · protein
Crystal structure of the hexameric purine nucleoside phosphorylase from bacillus subtilis in complex with tubercidin
4DAR · Purine nucleoside phosphorylase deod-type: “Crystal structure of the hexameric purine nucleoside phosphorylase from bacillus subtilis in complex with…”. X-ray diffraction, 1 ligand (TBN), 2 pockets (best druggability 0.57). MolNFT…
- PDB
- 4DAR
- Type
- protein
- Length
- 231 residues
- Chains
- 1
- 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
- TBN
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 231 | 35% helix, 28% strand | O34925 |
Ligands and binding sites
- TBN · 2-(4-amino-pyrrolo[2,3-d]pyrimidin-7-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.57 | 0.77 | 34 | TBN |
| 2 | 73 | 0.34 | 0.76 | 14 | empty |
Compared structures
- 4DAR · 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 4DAR · PDBe 4DAR · UniProt O34925
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