In 2009, the structure of P-glycoprotein (PDB ID 3G5U), a multidrug transporter and integral membrane protein, was solved at 3.8 Å resolution1; however questions arose as to whether or not this structure does indeed represent a physiological conformation. Recently, two further structures of P-glycoprotein were solved at 3.8 Å resolution 2, 3. These three structures each have a different assignment in the amino acid register of four of the twelve helices, giving three conflicting medium resolution structures. Using molecular dynamics simulation techniques, we have investigated the conformation and stability of the three structures in order to identify which structure best represents that of P-glycoprotein under physiological conditions. We find that, in a membrane environment, the conformation of the structures diverges from that of their respective crystallographic conformations; and the three alternate structures have varying degrees of stability and conformational flexibility. In contrast, molecular dynamics simulations of P-glycoprotein performed in the presence of the crystallization detergent show that P-glycoprotein maintains the crystallographic conformation 4. We characterize the differences in the membrane-embedded conformations of the three structures with respect to the experimental data to assess which structure best represents the physiological conformation of P-glycoprotein.