Color 1TPA by RMS differences between the BPTI complex and the apoenzyme. This will make BPTI red, because it is absent from the other layer. Blink through the models to compare their overall structure. Zoom in on catalytic triads and compare them. By now, you should be able to identify the specificity pockets of the three enzymes.
Display residues there, and compare the interiors of the pockets.
All three models are superimposed by Magic Fit . The catalytic triad is shown in wireframe, along with residues thought to be instrumental in activation of the zymogen. You can also turn off labels by shift-clicking any checkmark in the label column of the Control Panel , and if you do not alter the selections, you turn them back on again by clicking the heading of the label column. Compute H-bonds in all layers. Blink through the models.