Highlights ► The crystal structure of VctP from Vibrio cholerae N16961 was determined. ► Ferric-enterobactin and ferric-vibriobactin were positioned into the binding pocket. ► A basic triad of VctP balances the negative charges of ferric-enterobactin. ► A basic dyad of VctP balances the negative charges of ferric-vibriobactin.