how to reconcile PDB structures' sequences via Uniprot references?
None of them is integrase:

P12497
Protein    Gag-Pol polyprotein
Gene       gag-pol
Organism   Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1)

P14350
Protein    Pro-Pol polyprotein
Gene       pol
Organism   Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus)

Even if you meant the integrase product of the polyprotein, the second one is not even HIV.

From Wikipedia:


  Human Foamy Virus (HFV) is a retrovirus and specifically belongs to
  the genera Spumavirus. The spumaviruses are complex and significantly
  different from the other six genera of retroviruses in several ways.
  The foamy viruses derive their name from the characteristic ‘foamy’
  appearance of the cytopathic effect (CPE) induced in the cells.[1]