| BL | Blue-light |
| D450 | Dark state |
| DR | Dummy residue (which approximates amino acid residues in ab initio modeling for small-angle X-ray scattering data) |
| FMN | Flavin mononucleotide |
| LOV | Light-oxygen-voltage sensing domain |
| PAS | Per-Arnt-Sim |
| phot | Phototropin |
| phot1 | Phototropin1 |
| phot2 | Phototropin2 |
| PKA | Protein kinase A |
| S390 | Blue-light activated adduct state |
| SAXS | Small-angle X-ray scattering |
| SH2 | Src homology 2 domain |
| STK | Serine-threonine kinase domain |
| TEM | Transmission electron microscopy |
| WHD | Winged-helix domain |
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