MolNFT v1 · #122601 · protein
Crystal structure of E.COLI purine nucleoside phosphorylase with 7- deazahypoxanthine
5IU6 · Purine nucleoside phosphorylase deod-type: “Crystal structure of E.COLI purine nucleoside phosphorylase with 7- deazahypoxanthine”. X-ray diffraction, 2 ligands (7HX, SO4), 7 pockets (best druggability 0.62). MolNFT v1 #122601 on…
- PDB
- 5IU6
- Type
- protein
- Length
- 711 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- P0ABP8
- Ligands
- 7HX, SO4
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 37% helix, 28% strand | P0ABP8 |
Ligands and binding sites
- 7HX · 7H-pyrrolo[2,3-d]pyrimidin-4-ol · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.62 | 0.80 | 38 | 7HX, SO4 |
| 2 | 291 | 0.58 | 0.77 | 45 | 7HX, SO4 |
| 3 | 154 | 0.46 | 0.76 | 23 | 7HX, SO4 |
| 4 | 134 | 0.38 | 0.73 | 18 | empty |
| 5 | 81 | 0.35 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 130 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 130 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 125 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5IU6 · Crystal structure of E.coli purine nucleoside phosphorylase with 7-deazahypoxanthine · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABP8 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (P0ABP8) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P0ABP8
- Elsewhere: RCSB PDB 5IU6 · PDBe 5IU6 · UniProt P0ABP8
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