2OR1: Complex between 434 Phage Repressor and Target DNA
The structure to the right is that of Phage Repressor complexed with DNA. Use the following instructions to identify key characteristics of the complex:
1) Display the complex as wireframe, then select the DNA and display it as either Backbone or Ribbon.
2) Select all, and display as Cartoon
3) Select all, and display as wireframe. Now, select the protein and display it as spacefill.
4) Select all, and display as cartoon. Then select protein sidechains and display as ball and stick.
5) Select the helices and identify the loop part of the HTH motif.
6) Select the water residues and display as ball and stick.
7) Using a spacefill display for the DNA, and another display for the protein, try to identify a few residues that might be involved in VDW contacts. Find some nonpolar residues and display them as ball and stick to see if they're in touching distance.
As a result of the DNA-Protein interaction, the DNA is bent in an arc of radius ~65 A. This has two geometric consequences:
(1) Minor groove is compressed ~2.5 A at the center
(2) Minor groove widens ~2.5 A at the ends.