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FIG. 2. 3-D Structure of the trimeric AcrB and the binding of three substrates, ethidium, dequalinium, and ciprofloxacin. (A) A side view. Two of the three protomers are in front, and the remaining protomer is in the back. Part of the central cavity is visible through the vestibule (shown as an ellipse) that exists between the two protomers in front. Other features of the transporter, such as the central cavity, funnel, and pore, are described in the text. In the real complex, three drug molecules of the same structure were found in the AcrB trimer. In order to save space, a composite figure was generated from the structures bound with ethidium (gray), dequalinium (pink), and ciprofloxacin (yellow) (Protein Data Bank [PDB] files 1OY9, 1OYD, and 1OYF). We do not mean to imply that the binding cavity binds three different drug molecules at once (although this could occur). (B) A bottom view. The bound drug molecules can be seen within the central cavity. The positions of the vestibules are indicated. This figure was drawn with the program PyMOL (W. L. Delano, The PyMOL Molecular Graphics System; Delano Scientific, San Carlos, Calif.; www.pymol.org).
