In the vast majority of cases you cannot turn a PDF into spatial data, except for georeferencing it as an image. There are some exceptions, such as when the PDF already includes georeferenced vector data, but its very unlikely you had that sort of file given the issue you described.

You likely either: - needed to export an image of the data (raster); - needed to digitise the data within; - needed to extract the vector data first from the pdf and work out how to deal with it.

Opening a pdf without appropriate data structures into a gis software package is akin to taking a picture of a billboard that has a printed image of a map on it and then expecting to be able to do anything with that picture. The pdf is a bit better, but not by much unless it began life as a georeferenced pdf with vector data maintained.