Sure. So, say you have a canon origfic where your protagonists are the cops and the antagonists are the mob. You would then write an AU where your cop characters are the mob, and the mob characters are the cops. OR, I could see interpreting it as rewriting it so the mobsters are the protagonists and the cops are the antagonists (switching the protag and antagonism just by point of view/extra information on motives, etc.).

If you don't have a particular 'verse already where you've got protagonism and antagonism set up, I'd say that just picking a "traditional" setup (angels vs. demons, cops vs. robbers, etc) and writing it with a nontraditional protagonist/antagonist slant would work fine, too. Make sense?