Abstract

Factor D, an essential enzyme for the activation of the alternative pathway of the complement system, belongs to the serine protease superfamily. The crystal structure of the enzyme was solved by a combination of multiple isomorphous replacement and molecular replacement methods. The present model was refined to an R-factor of 18.8%...
The two non-crystallographically related molecules in the triclinic unit cell have distinct active site conformations. The protein has the general structural fold of a serine protease, but there are several unique amino acid substitutions resulting in significant alterations in the critical loops responsible for catalysis and substrate specificity in serine proteases. Factor D is the first complement serine protease whose three-dimensional structure has been determined.

Figure 9 (top) Superposition of catalytic residues (57, 102 and 195) for molecule A (magenta) and molecule B (cyan).
Figure 10 (bottom). The structure of trypsin (deep blue) is compared with that of molecule A (magenta) and molecule B (cyan).

(note, these figures aren't exactly the original figures in the article, but very similar ones made for the Atlas of Protein Structure still online).