What type of animation software is used to create these molecular motor motions?
Most any reasonable animation/modeling software can handle this sort of animation. I have developed an educational iOS app with interactive biological macromolecules, including several animations. Here is how I would approach this, I suspect something similar was done here.

The models are likely built up from PDB files, or equivalent. These files allow viewing and manipulating large molecules in 3D with special viewers.  Many 3D modeling/animation apps can also view and convert these molecules into polygonal models that can be used as components and then animated within the app. I use Cinema 4D, not cheap. There is a free, downloadable program called Blender. I'm sure Blender can handle the animation but not certain whether it can read and convert the PDB file. If not, there may be other options for this.

This is not a challenge to be taken lightly. The person doing the animation you reference also knew how to assemble the parts as well as how the movement is effected. There is also a steep learning curve to using this type of software.