Papain, chymotrypsin a, chymotrypsin B, papain peptidase B and other proteolytic enzymes were found in the immature fruit of papaya. The primary structures of the four cysteine proteases are highly homologous. Among them, Papain is a sulfhydryl protease, which can hydrolyze the carboxyl ends of arginine and lysine in proteins and peptides, and can preferentially hydrolyze those amino acids with two carboxyl groups or aromatic L-amino acids at the N-terminal of peptide bond.

Papain is a proteolytic enzyme with molecular weight of 23406. It is composed of a single peptide chain and contains 212 amino acid residues. There are at least three amino acid residues in the active center of the enzyme, cys25, his159 and asp158. When cys25 is oxidized by oxidant or combined with metal ions, the enzyme activity is inhibited, while the reductant cysteine (or sulfite) or EDTA can restore the enzyme activity. The other six cysteine residues form three pairs of disulfide bonds, which are not in the active site. Pure papain products can contain: (1) papain with molecular weight of 21000, accounting for 10% of soluble protein; (2) chymopapain with molecular weight of 26000, accounting for about 45% of soluble protein; (3) lysozyme with molecular weight of 25000, accounting for about 20% of soluble protein; and cellulase and other different enzymes.