Fig. 5

Modeling of HERV-K protease: a alignment of HERV-K with HIV-1 protease (2HS1) and Rous sarcoma virus protease (1BAI). Red boxes mark residues totally conserved in the three sequences and red residues boxed in blue are highly similar residues. b Ribbon representation of the HIV-1 protease dimer (2HS1) used as a main template in the modeling. Strands are colored in yellow, loop in gray, turn in blue, and α-helices in red. Active site residues are represented with their carbon atoms colored in cyan, nitrogen in blue and oxygen in red. c Model of HERV-K protease, carbon atoms of the conserved residues of the active site are colored green and non-conserved red