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.

The models were energy minimized to remove possible steric hindrances if any which could lead to instability of the enzyme. The surface electrostatic potential of the CEPA structure helps to analyze local charges near binding sites.