FIGURE 7.
The native secondary structure and tertiary structure of the protein S15 binding fragment of 16S rRNA. (A) Its native secondary structure. (B) Its native tertiary structure as observed in X-ray crystallography (PDB 1DK1; http://www.wwpdb.org/). The helices are numbered from 1 to 5 in the direction from the 5′ end to the 3′ end, and are colored in the order of magenta, green, yellow, blue, and cyan, respectively. The three-way junction is colored in red, which contains a base triple and the metal binding site. In addition, local strands in this junction are in the parallel direction instead of the canonical antiparallel direction. (C) The tertiary structure predicted by pk3D, plotted in the same color code as in B. The spatial arrangement of helices 3–5 are predicted correctly. The overall position of helix 1 is only roughly correct, tilted at a different angle.