Fig. 4: MD simulations of apo ACOX-1.1 showing opening of the FAD and ATP-binding sites.

a Representative structures from the MD simulations of the apo enzyme with an open versus a closed FAD-binding site. For the apo enzyme with the FAD site in the open state, subunit A is in orange and subunit B is in cyan. For the apo enzyme with the FAD site in the closed state, both subunits are in white. b Comparison of a surface view of the representative structures of the apo enzyme from (a) showing an open and closed FAD-binding site. c Representative structures from the MD simulations of the apo enzyme with an open versus a closed ATP-binding site. For the apo enzyme with the ATP site in the open state, subunit A is in orange and subunit B is in cyan. For the apo enzyme with the ATP site in the closed state, both subunits are in white. d Comparison of a surface view of the representative structures of the apo enzyme from (c) showing an open and closed ATP-binding site. a–d The representative structures shown were obtained from the most populous clusters from clustering analysis of the MD simulations performed as described in “Methods”. a–d ATP and FAD have been modeled into the structures based on their positions in the holo ACOX-1.1(E434A) crystal structure.