MolNFT v1 · #18506 · protein
Escherichia COLI purine nucleoside phosphorylase complexed with 9- beta-D-ribofuranosyl-6-methylthiopurine and PHOSPHATE/SULFATE
1PR4 · Purine nucleoside phosphorylase deod-type: “Escherichia COLI purine nucleoside phosphorylase complexed with 9- beta-D-ribofuranosyl-6-methylthiopurine…”. X-ray diffraction, 2 ligands (MTP, PO4), 7 pockets (best druggability 0.58).…
- PDB
- 1PR4
- Type
- protein
- Length
- 703 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
- P0ABP9
- Ligands
- MTP, PO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 232 | 36% helix, 29% strand | P0ABP9 |
| B | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 37% helix, 27% strand | P0ABP9 |
| C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 234 | 35% helix, 29% strand | P0ABP9 |
Ligands and binding sites
- MTP · 2-hydroxymethyl-5-(6-methylsulfanyl-purin-9-yl)-tetrahydro-furan-3,4-diol · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.58 | 0.77 | 36 | PO4, MTP |
| 2 | 241 | 0.56 | 0.78 | 35 | PO4, MTP |
| 3 | 223 | 0.54 | 0.77 | 36 | PO4, MTP |
| 4 | 133 | 0.39 | 0.74 | 18 | empty |
| 5 | 64 | 0.33 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 134 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 117 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 112 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1PR4 · Escherichia coli Purine Nucleoside Phosphorylase Complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABP9 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (P0ABP9) · a predicted model of the same protein · chain C 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 P0ABP9
- Elsewhere: RCSB PDB 1PR4 · PDBe 1PR4 · UniProt P0ABP9
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