Figure 6.  A comparison of four different types of HIV-1 RT structures.  The alpha-carbon backbones of four different types of HIV-1 RT structures (unliganded, NNRTI bound, DNA bound, and DNA and incoming dNTP bound) are shown as colored ribbons (the key is given in the figure).  The ligands have been omitted from the figure to simplify the comparisons of the HIV-1 RT structures.  Although all of the subdomains of the p66 subunit and the RNaseH domain move relative to the core of the enzyme when ligands or NNRTIs bind to the enzyme, the greatest movements involve the fingers and thumb.  The position of the thumb in the two DNA-bound forms (binary and ternary) is similar; however, the position of the thumb is moderately different in the NNRTI-containing structure, and very different in the unliganded structure.  There are significant differences in the position of the fingers subdomain in the four structures - in particular, in the position of the beta3-beta 4 loop of the fingers.  This loop closes down on the incoming dNTP in the ternary complex.  The superposition was produced using the program PROFIT with five points fixed: two in the polymerase active site, residues 100-200 and 400-420 of the p51 subunit, and the RNaseH domain.  To look at the structure comparison in more detail, the PDB file for the comparison of the four structures can be downloaded here (4rts1.pdb).