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I’m trying to reconcile structures in PDB entries with their sequences as reported in their chemList.polymer.dbref entries.

E.g.: considering structures for HIV integrase:

PDB:3OS0 references UNP:P14350, focusing on integrase (len=391)

>sp|P14350|752-1143
CNTKKPNLDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQ…NRTVSIDNLKPTSHQNGTTNDTATMDHLEKNE 

PDB:2B4J references UNP:P12497, focusing on integrase (len=287)

>sp|P12497|1148-1435
FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGI…LLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED

Why should these sequences be so different?!

and in case you think I'm focused on a bit of noise: there are 42 other HIV integrase structures all referencing UNP:P14350, and 43 other structures referencing UNP:12497 (and 79 others referencing UNP:Q76353, very similar to UNP:12497), 22 referencing an entirely different UNP:Q72498.

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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]

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