MolNFT v1 · #118997 · protein
Binding and structural studies of a 5,5-difluoromethyl adenosine nucleoside with the fluorinase enzyme
5FIU · 5'-fluoro-5'-deoxy-adenosine synthase: “Binding and structural studies of a 5,5-difluoromethyl adenosine nucleoside with the fluorinase enzyme”. X-ray diffraction, 1 ligand (Y3J), 10 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5FIU
- Type
- protein
- Length
- 873 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-fluoro-5'-deoxy-adenosine synthase
- EC
- 2.5.1.63
- UniProt
- Q70GK9
- Ligands
- Y3J
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 5'-fluoro-5'-deoxy-adenosine synthase (EC 2.5.1.63) | protein | 291 | 22% helix, 30% strand | Q70GK9 |
Ligands and binding sites
- Y3J · 5,5-difluoromethyl adenosine · ligand · 3 copies · chains A, C, B
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.80 | 0.98 | 27 | TLA, Y3J |
| 2 | 653 | 0.79 | 0.84 | 77 | empty |
| 3 | 121 | 0.79 | 0.97 | 28 | Y3J, TLA |
| 4 | 111 | 0.78 | 0.97 | 27 | TLA, Y3J |
| 5 | 251 | 0.69 | 0.85 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1652 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1643 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1632 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5FIU · Binding and structural studies of a 5,5-difluoromethyl adenosine nucleoside with the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q70GK9 · AlphaFold monomer V2.0 prediction for 5'-fluoro-5'-deoxy-adenosine synthase (Q70GK9) · 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 Q70GK9
- Elsewhere: RCSB PDB 5FIU · PDBe 5FIU · UniProt Q70GK9
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