We don't know a whole lot about it other than it was described as a 46-gun ship in the Spanish service. Henry Every, who mutinied and stole the ship from its captain at the Groyne, is supposed to have had it razeed (which is a term of art for cutting down the superstructure and top-hamper -- sometimes it means turning a two-gun-deck ship into one). But we don't know what was done to that ship in particular -- whether it was cut down into a single-deck ship, or just had superstructure removed.

There are what are described as contemporary views of it, one of which is on Wikipedia, where it looks a bit like a galleon-type ship, which were still hanging around in the late 17th century (that is, with a high stern-castle and significant tumblehome), but the provenance of a lot of those is uncertain and they were meant as illustrations in lurid tales about pirates, not as evidence of what the ship looked like.

In terms of whether it was a fifth or sixth rate, those were distinctions that were peculiar to the English navy. Fifth and sixth rate ships were called frigates, but any warship could be a called a man of war; if this ship were in the English service, 46 guns would place it in the fourth rate. Again, we don't know how many guns it had before being razeed; 46 is the assumption for after.