This particular PDB entry was used in making the starting structure used in modeling1 the mechanism for the hydrolysis of proteins by chymotrypsin. The various steps in the mechanism are available for download.
1: Stewart, J. J. P. (2017). "An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin." Journal of Molecular Modeling 23(5): 154.
Abstract
The catalytic cycle for the serine protease α-chymotrypsin was
investigated in an attempt to determine the suitability of using the
semiempirical method PM7 in the program MOPAC for investigating
enzyme-catalyzed reactions. All six classical intermediates were modeled
using standard methods, and were characterized as stable minima on the
potential energy surface. Using a modified saddle point optimization method,
five transition states were located and verified both by vibrational and by
intrinsic reaction coordinate analysis. Some individual features, such as
the hydrogen bonds in the oxyanion hole, the nature of various electrostatic
interactions, and the role of Met192, were examined. This involved designing
and running computational experiments to model mutations that would allow
features of interest, in particular the energies involved, to be isolated.
Three features within the enzyme were examined in detail: the reaction site
itself, where covalent bonds were made and broken, the electrostatic effects
of the buried aspartate anion, a passive but essential component of the
catalytic triad, and the oxyanion hole, where hydrogen bonds help stabilize
charged intermediates. With one minor exception, all phenomena investigated
agreed with previously-reported descriptions. This result, along with the
fact that all the techniques used were relatively straightforward, leads to
the recommendation that PM7 and related methods, such as PM6-D3H4, are
appropriate for modeling similar enzyme-catalyzed reactions.