The large domain consists of an anti-parallel beta-sandwich and a short haem-binding peptide, which form a three-layer structure.

The haem nestles between two short helices at the N terminus of cyt f. Within the second helix is the sequence motif for the c-type cytochromes, CxxCH (residues 21–25), which is covalently attached to the haem through thioether bonds to Cys-21 and Cys-24.

The sixth haem iron ligand is the alpha-amino group of Tyr-1 in the first helix.

[2] Cyt f has an internal network of water molecules that may function as a proton wire.

[2] The water chain appears to be a conserved feature of cyt f.