The secondary structures of the enzyme have folded into 10 helices and 11 beta-sheets connected by loops. The active site of cepA includes the Ser70, Lys73, and Glu166 sites within the core pocket. The catalytic motifs and loops present in the neighboring sites are conserved in all the enzyme variants.

As a part of structure validation, Ramachandran plots were constructed for each of the variants and the presence of any residues in the disallowed regions was confirmed. Out of 23 variants, 4 of them showed 0.04% residue in the disallowed region, and aspartate at position 227 slightly shifted to the disallowed region in these four cases and was ignored for any modifications.