You can use standard molecular modelling apps like UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or pymol to open the structure and export it as VRML, X3D, or OBJ. Then open that file in the free Meshlab (http://meshlab.sourceforge.net/) and export as Collada.
iBooks author seems to prefer Collada version 1.4 over 1.5 files, and likes the mesh to be triangulated.
Be aware that your representation options in the molecular modelling app (ribbon, space-filling, surface etc.) will determine what geometry is exported.
For a much more flexible experience, look into Molecular Maya, ePMV, or Bioblender, which are plugins for Maya, Cinema4D, and (the free and open source) Blender to add molecular modelling functionality directly within those environments.
As well: iBooks Author: Best practices for using 3D models