The Pepsin molecule - rotatable in 3 dimensions

Pepsin is a protease (protein-digesting enzyme), which is active in the stomach.

The porcine pepsin molecule displayed here consists of 327 amino acid residues - 5053 atoms, now including hydrogen atoms, but this also includes oxygens from 375 water molecules!

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

There are several aspartyl protease enzymes with a broadly similar structure to mammalian pepsin, not all of which are strictly digestive in function:

Web references

Analysis of crystal structures of aspartic proteinases: On the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes Natalia S. Andreeva and Lev D. Rumsh

The pepsin residue glycine-76 contributes to active-site loop flexibility and participates in catalysis. Okoniewska M, Tanaka T, Yada RY.

Pepsin From Wikipedia, the free encyclopedia