Research workbench
Crystal structure of E. COLI purine nucleoside phosphorylase complexed with 2-fluoroadenosine and SULFATE/PHOSPHATE
Analyse Crystal structure of E. COLI purine nucleoside phosphorylase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PK9
- 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
- P0ABP9
- Ligands
- 2FA, PO4
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 36% helix, 27% strand | P0ABP9 |
Ligands and binding sites
- 2FA · 2-(6-amino-2-fluoro-purin-9-yl)-5-hydroxymethyl-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 | 347 | 0.60 | 0.77 | 49 | PO4, 2FA |
| 2 | 242 | 0.59 | 0.80 | 38 | PO4, 2FA |
| 3 | 248 | 0.54 | 0.76 | 38 | PO4, 2FA |
| 4 | 81 | 0.33 | 0.75 | 16 | empty |
| 5 | 61 | 0.33 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 126 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 121 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 104 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1PK9 · 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 1PK9 · PDBe 1PK9 · UniProt P0ABP9
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