So I'm trying to get a more current answer to these questions because the only papers I can find are from over a decade ago and this field is moving too fast to take them at face value.

 

So how many protein coding genes are there in the human genome? (HGP)

How many of these do we have experimental evidence for? (UniProt?)

and how many of these do we have an experimental structure for? (PDB?)

 

Help and links would be greatly appreciated

Well 1) has not been resolved yet and is still very much an estimate. For 2+3 I would simply go to the indicated databases and perform a search and limit it to Homo sapiens as qualifier. That should give you the number based on what is in the given database. One should note that not all experimental evidence is equal. Some entries are based on sequence similarity based on evidence in other organisms (which may or may not be accurate). Or some evidence is very weak (though it would take a lot of digging to figure it out).