X-ray structure of an E. coli trp repressor–operator–tryptophan complex. The complex is viewed with its molecular 2-fold axis horizontal. The protein's two identical subunits are drawn in ribbon form colored pink and blue with their helix–turn–helix (HTH) motifs more deeply colored. The 18-bp-containing self-complementary dsDNA is shown in stick form with C gray, N blue, O red, P orange, and with successive P atoms in the same chain connected by orange rods. The trp repressor binds its operator only when l-tryptophan, drawn in space-filling form with C green, is simultaneously bound. Note that the protein's recognition helices (the longer HTH helices) bind, as expected, in successive major grooves of the DNA but extend approximately perpendicular to the DNA duplex axis. In contrast, the recognition helices of 434 repressor protein are nearly parallel to the major grooves of their bound DNAs (Interactive Exercise 39). Click the "Show HTH Motif" button to more closely view the interaction between the HTH motif and the DNA. Here the protein side chains that interact with the DNA are drawn in stick form with C cyan, N blue, and O red. Clicking on the "Show HTH Motif" button a second time shows the hydrogen bonds between the HTH motif and the DNA (dashed black lines) together with their lengths. [Based on an X-ray structure by Paul Sigler, Yale University. PDBid 1TRO.]