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Page 1 (in Ch.7) Page 2 Tertiary Structure; Substrates Page 3 Active Site
Page 5 Reaction Mechanism Page 6 Crystal Structures Page 7 References

An example of an active site: the serine proteases

Summary of highlighted residues in chymotrypsin

                                                   in loop
                                                   between   colour in
                                          domain   strands:  diagrams
                                          ______   ________  _________

Catalytic Triad        His-57  side chain   1          3,4      red
                       Asp-102 side chain   1          5,6
                       Ser-195 side chain   2          3,4

Oxyanion Hole          Gly-193 main chain   2          3,4      white
                       Ser-195 main chain   2          3,4

Specificity Pocket     Ser-189 side chain   2          5,6      green
                       Gly-216 side chain   2          5,6
                       Gly-226 side chain   2          3,4
                               

Main Chain             Ser-214 main chain   2          5,6      yellow
   Substrate Binding   Trp-215 main chain   2          5,6
                       Gly-216 main chain   2          5,6

Tripeptide cleavage                                             blue
   product

The following diagrams are of chymotrypsin complexed with a tripeptide (crystal structure 8gch). This tripeptide (Gly-Ala-Trp) is in fact a product of autolysis, i.e. a peptide fragment produced by the hydrolysis of chymotrypsin by another chymotrypsin molecule; refer to Part 1 . The large tryptophan side chain is situated inside the specificity pocket.

(Crystallography note: numerous different types of peptide fragment occurred in different chymotrypsin molecules in the protein crystal; this tripeptide results from the overlapping electron density of different asymmetric units.)

Views are shown both with and without the tripeptide fragment.

A view looking into the substrate-specificity pocket, without tripeptide:

close up

The same view with tripeptide:

close up

a different view to illustrate the main-chain hydrogen bonding to the substrate/product

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J. Walshaw