Circadian clock proteins or Circadian clock protein kinase measure out the 24 hour circadian rhythm. In cyanobacteria protein KaiA[1] stimulates KaiC[2] which adds phosphate groups to itself. Then KaiC binds to KaiB[3] which inactivates KaiA and causes the number of phosphate groups on KaiC to drop slowly. KaiB disconnects allowing KaiA to start the cycle again.[4] For details of KaiC see Circadian Clock Protein KaiC.
Circadian clock protein KaiA from Synechococcus elongatus is (PDB entry 1r8j).
3D Structures of circadian clock protein
Circadian clock protein 3D structures