MolNFT v1 · #18300 · protein
Crystal structure of E. COLI purine nucleoside phosphorylase complexed with 2-fluoro-2'-deoxyadenosine and SULFATE/PHOSPHATE
1PKE · Purine nucleoside phosphorylase deod-type: “Crystal structure of E. COLI purine nucleoside phosphorylase complexed with 2-fluoro-2'-deoxyadenosine and…”. X-ray diffraction, 2 ligands (2FD, PO4), 6 pockets (best druggability 0.60).…
- PDB
- 1PKE
- Type
- protein
- Length
- 706 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
- 2FD, PO4
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 35% helix, 28% strand | P0ABP9 |
| C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 232 | 34% helix, 28% strand | P0ABP9 |
Ligands and binding sites
- 2FD · 5-(6-amino-2-fluoro-purin-9-yl)-2-hydroxymethyl-tetrahydro-furan-3-ol · 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.60 | 0.77 | 46 | PO4, 2FD |
| 2 | 231 | 0.56 | 0.78 | 34 | PO4, 2FD |
| 3 | 252 | 0.53 | 0.76 | 37 | PO4, 2FD |
| 4 | 74 | 0.36 | 0.77 | 15 | empty |
| 5 | 73 | 0.32 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 116 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 91 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1PKE · Crystal Structure of E. 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 1.00
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 1PKE · PDBe 1PKE · UniProt P0ABP9
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