Fig. 4: Allosteric MK-9 binding site of cyt. bdMtb. | Nature Communications

Fig. 4: Allosteric MK-9 binding site of cyt. bdMtb.

From: The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB

Fig. 4

a Left: Side view closeup of the MK-9 binding pocket composed of residues from TMH1, TMH9, and the heme b595 porphyrin scaffold. Right: Front view closeup of the MK-9 binding pocket composed of residues from TMH1, TMH9, and the heme b595 porphyrin scaffold. Van-der-Waals interaction distances are indicated. b Representative snapshots of different MK-9 binding modes during 2 × 750 ns MD simulations in reduced and oxidized states. For simplicity, hydrocarbon chains of MK-9 molecules are not shown. c Distance histograms between MK-9 and heme b595 (Top), and MK-9 and Trp9.A (Bottom) during MD simulations. Blue data plots indicate a simulation setup with reduced MK-9. Green data plots indicate a simulation setup with oxidized MK-9. Oxidized MK-9, green; reduced MK-9, blue; heme b595, purple; Trp9.A, yellow.

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