Benchmark cases analysis. (a) Structural superposition of the S. cerevisiae (red) and the E. coli (blue) chorismate mutase (PDB code 4csm and 1ecm, respectively). These two patches align ten residues, with a resulting Z-score of 15.76. (b) Structural superposition of the 4-hydroxyphenylpyruvate dioxygenase (PDB code 1cjx, red), the 2,3-dihydroxybiphenyl 1,2-dioxygenase (1han, blue), catechol 2,3-dioxygenase (1mpy, green) and the methylmalonyl-Coa epimerase (1jc5, yellow). The 1han co-crystallized iron ion is shown. (c) Superposition of the tumor necrosis factor-alpha-converting enzyme (1bkc, red) and the peptide deformylase (1icj, blue). The 1icj co-crystallized nickel ion is shown. (d) Structural superposition of the human P21 ras protein (5p21, red) and HprK/P 1jb1 (blue). (e) Structural superposition of the 1b37 FAD-binding pocket (red) with the highest-score matches obtained in a database search (blue). The 1b37-bound FAD is shown. (f) Bound ligands superposition. Using the three-dimensional transformation used to superpose the residues aligned in (e), also ligands that are bound to some of these proteins are consequently superposed. The ADP molecule bound to the 1djn patch nicely matches the ADP moiety in the similar FAD-binding pockets.