Analysis of model 6 and creation of the dimeric model 7 HIV-1 CRF02_AG IN structure.

<p>(A) Domain organization of HIV-1 and PFV IN domains showing regions of structural and sequence overlap as well as structural gaps. (B) Structural alignment of modeled chain A (yellow) aligned with templates 3OY9 (cyan) and 1EX4 (dark green); (C) Comparative Verify3D analysis of the two templates with model 6; (D) Modeled Chain B (yellow) is aligned to PFV chain B (light green) and non-overlapping segments have been removed; (E) Dimeric CRF02_AG IN structure (pink and green cartoon) overlays well with the dimeric PFV structure (shown as sticks) with a global RMSD <1.5Å. With the exception of carbon atoms, all coloration of the PFV stick structure is based on the Corey-Pauling-Koltun (CPK) coloration scheme [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128310#pone.0128310.ref018" target="_blank">18</a>]; white for hydrogen, blue for nitrogen, and red for oxygen.