Figure 2:

Comparison of the deep binding pocket of AcrB wildtype, AcrB V612F and OqxB. a. Upper panel: Side view of the trimer structures of AcrB, OqxB, and AcrB V612F with each monomer coloured corresponding to the conformational state (L state in blue, T state in yellow and O state in red). The AcrB wildtype (left) has been crystallised in the LLL and LTO states (PDB ID: 1iwg and 4dx5, respectively) whereas OqxB (middle) has been crystallised in the TTT state (PDB ID: 7cz9). Here we show that both AcrB V612F (right) and V612W (Fig. S4) crystallise in the TTT state. Lower panel: top view of the deep binding pocket in the T state with conserved deep binding pocket residues shown as sticks. Crystallographic 2Fo-Fc densities are depicted as a mesh contoured at 1 σ. The residues at positions 610 and 612 in AcrB and the corresponding positions 616 and 618 in OqxB are highlighted in red. b. Overlay of the minocycline binding pose in the experimental structures of AcrB wildtype (grey, PDB ID: 4dx5) and V612F (yellow). The residue at position 612 is shown as sticks. c. Minocycline interactions in the deep binding pocket of AcrB wildtype (PDB ID: 4dx5) and V612F. The crystallographic 2Fo-Fc maps are shown at σ 1 (mesh) and the densities for minocycline are highlighted in red. Minocycline and residues with at least one atom within 4 Å distance of the ligand are shown as sticks and indicated with single letter amino acid code and position number. The interaction (dashed lines) and distances between the side chains and minocycline are indicated. Carbon atoms are given in grey, oxygen in red, and nitrogen in blue.