Visualizing a binding site.
The example shown above is the ternary complex of dihydrofolate reductase, methotrexate and NADPH (from PDB code 3dfr).
a. The surface of the protein is shown as a shaded sketch, with the methotrexate molecule (on the left) and NADPH molecule (on the right) emerging into visibility here and there. The invisible parts of the two molecules are represented by dotted lines.
b. All the gap regions (cavities and grooves) in the protein are shown by the purple wire cage surface. They are generated as described here.
c. Just the gap regions, with the protein removed. The two bound molecules can be seen within the largest of the gap regions.
d. The largest of the gap regions, corresponding to the protein's binding site, is shown on its own, extracted from all the rest by the program MASK.