Figure 3.

Three distinct conformations of the matrix-metalloproteinase active site, extracted from an molecular dynamics simulation. Some protein residues have been removed to facilitate visualization. The protein is shown in gray, the active-site zinc cation is shown in ice blue, and the ligand is colored by element. (A) Some protein conformations were not amenable to fragment addition. (B) Other conformations were amenable to fragment addition but did not allow deep binding to the S1′ subsite. (C) Others were amenable to both fragment addition and deep binding.