Unlike a PDF, a Fixed Layout book is a true eBook. It uses the ePub file format and can be sold and purchased through online eBook retail stores. Fixed Layout eBooks utilize two-page spreads and the page turn animations in the iPad to give you the look and feel of holding a real book in your hands.
PDFs, on the other hand, cannot be purchased through online bookstores. You can view and save a PDF on your device, but it does not have the full display capabilities of a Fixed Layout eBook.