Fig. 4: Binding of fragment 048 to P pocket. | Nature Communications

Fig. 4: Binding of fragment 048 to P pocket.

From: Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket – targeting P-pocket by fragment screening

Fig. 4

a The chemical structure of fragment 048. b Polder map at 4.5σ contour defines the binding mode of 048 to P-pocket. c The binding mode of 048 is distinct from that of 166. d LigPlot showing a 2D representation of interactions of 048 with nearby residues and nucleotides. e The binding of 048 caused expansion and rearrangement as revealed by comparing P-pocket of apo P-1 complex (dark gray) and 048-bound P-1 complex (light-gray RT, green primer, and yellow template); the shifts of key motifs in the pocket are indicated by dotted red arrows. The rmsd for the pocket residues is 1.2 Å. f Fragments 166 and 048 occupy different parts of P-pocket.

Back to article page