Transporters are the gatekeepers of the cell that serve vital homeostatic and protective roles for the membrane. We use cryo-EM and biophysical approaches to understand how they are regulated, which often involves difficult to trap intermediates of disordered or flexible domains. Our structure of BmrCD, a bacterial drug transporter, traps never before seen ternary complex bound with substrate and ATP. Another related structure of Yeast Cadmium Factor 1, a fungal metabolite transporter, reveals how a disordered domain is ordered upon phosphorylation to impact the central transporter architecture.