HIVToolbox, an Integrated Web Application for Investigating HIV
(A–C) Output of HIVToolbox showing relationships of IN elements shown in a model constructed from superposition of the catalytic domains in structures 1EX4 and 1K6Y. Residues 1–7, 47–55, 140–148, and 270–288 are unstructured and not shown. The left panels shows domains [NTD (red), CCD (Blue), and CTD (green)] and minimotifs; the center panels show functional sites and protein-protein interactions the right panels shows residues that are >98% conserved in 3787 HIV-1 IN isolates (yellow). (A) Location of three of the four putative CK2 phosphorylation sites located on the surface of the IN CCD (left panel); the 4th CK2 site is in the CTD unstructured region. Numbers indicate the positions of putative phosphorylation sites. D270 is the last residue in the structure (orange). Conservation of the residues on CK2 sites is shown in Table 1. (B) Conservation and location of the dimerization interface(s). Residues at the dimerization interface less than 3.25 Å from atoms in the other chain are colored: (red, 1EX4), (cyan, 1WJA), and (lighter cyan, 1K6Y). (B, C) Conservation and location of protein-protein interaction sites, modification sites, and DNA binding sites. (C) is a 180° rotation of (B) about the z-axis. (A, B, C) Sites are colored: DNA binding = green, Importin 7 binding = dark purple and dark green, Zn binding = purple, Karyopherin α5 binding = teal and orange, LEDGF binding = teal, Lysine acetylation = dark green, proline isomerization = orange, active site = royal blue, reverse transcriptase (RT) binding = brown.