3D Structure of Human Pepsin

CPK Color Scheme

On this page, you can see a 3-dimensional depiction of Human Pepsin A, a protein central to the breakdown of proteins in the human gut. The large active site can be seen easily as the molecule rotates.

Reset and rotate the molecule.

View pepsin with an inhibitor, pepstatin, highlighted in the active site.

For the rest of the displays, this inhibitor will be left more or less invisible. Click here to see pepsin in this form.

Pepsin's ability to persist without denaturing in extremely low pHs is in large part because of its amino acid makeup. It only has 4 basic (in terms of pH) amino acids, 3 arginines and 1 histidine. The histidine are shown here in yellow and the arginines in red.

In contrast, pepsin has 44 acidic amino acids in the form of glutamic acids and aspartic acids which help to keep the protein stable in its acidic environment. The glutamic acids are marked in yellow with the aspartic acids in red.

This displays the secondary structure of pepsin, with α-helices in yellow and β-sheets in red. In order to maintain its stability in an acidic environment, pepsin is made up mostly of β-sheets since β-sheets interact with and stabilize one another more readily than α-helices.

Here the catalytic regions of the active site are highlighted in green.

Here are the main components of the pepsin molecule. The active site is now in pink with the crucial Asp 32 and Asp 215 residues in white. If either of these aspartic acid residues is changed, the pepsin enzyme is nonfunctional. The active site flap is yellow, the S1 subsite is green. The S1 subsite is one of the locations where molecules recognized by the protein will bind while another part of the molecule is interacting with the active site.

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