The molecule has a deep cleft, the bottom of which contains the active site. This contains a pair of aspartate residues on either side of the cleft which break peptide bonds in proteins by the addition of water: -H to one side and -OH to the other. It is said that pepsin will preferentially break peptide bonds next to aromatic amino acids such as phenylalanine and tyrosine, but not next to valine, alanine or glycine. It does not therefore necessarily break down proteins into individual amino acids.
Pepsin is secreted as an inactive precursor
pepsinogen.
Primary structure
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Secondary structure
Cartoon format - α helices red, β sheets gold
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Tertiary structure
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Active site
Aspartate residues 32, 215 in active site
Water in active site
Glycine residue 76 in flap above active site