Research workbench
Fluorinase substrate flexibility enables last step aqueous and ambient 18F fluorination of a rgd peptide for positron emission tomography
Analyse Fluorinase substrate flexibility enables last step aqueous and ambient 18F… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CQJ
- 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
- EFA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 29% 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 | 21% helix, 29% strand | Q70GK9 |
Ligands and binding sites
- EFA · 5'-deoxy-2-ethynyl-5'-fluoroadenosine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.82 | 0.89 | 57 | empty |
| 2 | 375 | 0.79 | 0.89 | 58 | EFA |
| 3 | 383 | 0.78 | 0.87 | 66 | EFA |
| 4 | 132 | 0.76 | 0.94 | 29 | EFA |
| 5 | 340 | 0.70 | 0.83 | 48 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1698 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1632 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1587 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4CQJ · Fluorinase substrate flexibility enables last step aqueous and ambient 18F fluorination… · 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 A 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 4CQJ · PDBe 4CQJ · UniProt Q70GK9
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