This enzyme is found in mitochondria, but the details vary according to the source. The chicken enzyme, shown here has two similar membrane spanning proteins, with 3 long alpha-helices each. Two proteins are peripheral to the membrane. They contain the active site and electron transfer cofactors.

The large peripheral protein contains the flavin gopup, FAD. This is at the catalytic site. Next is a 2Fe2S center, then a 4Fe4S center, and finally a 3Fe4S center. These are all housed in the smaller peripheral subunit, the FeS protein. In the integral membrane subunits are found the substrate ubiquinone, and a heme. A molecule of phospholipid (PE) is also shown. It seems to play a structural role.

Zoom into the catalytic site. The flavin and 3 Fe-S centers are now colored white. A substrate analog is shown in wireframe. It sits very close to the flavin. It is hydrogen bonded by several residues, including the 2 Arg and 2 His that are shown.