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. 2014 Dec 23;59(1):310–316. doi: 10.1128/AAC.04274-14

FIG 5.

FIG 5

Homology model of HIV-1 integrase subtype B. A homology model was generated based on the crystal structure of the target capture complex of PFV (PDB identification no. 4E7K). Secondary structure overlays and catalytic triad orientations and positions were examined for WT and mutant HIV-1 integrases. (A) Global overlay of the INWT, INH51Y, and INR262K/H51Y models. (B and C) Close-up overlays, showing the relative positions of the catalytic triad of D64, D116, and E152 in INWT (B and C), INH51Y (B), and INR262K/H51Y (C) coordinating Mn2+ ions. Mn2+ ion positions were simulated by inserting their coordinates from the PFV structure (PDB identification no. 4E7K) in the active site, and the ions are represented as small black spheres. Coordinates of the viral LTR and target DNA were inserted in the active site of the integrase homology models by overlap of the PFV crystal structure (PDB identification no. 4E7K). All images were processed using PyMOL software. Diagrams and carbon atom coloration differentiate the INWT (white), INH51Y (black), and INR262K/H51Y (gray) homology models.