structure

What is Structure?
The NCBI Structure database contains three-dimensional depictions of biomolecules. These can be viewed and manipulated using a program called Cn3D, which is freely available to us.

Tips for using Structure:

The Cn3D interactive display includes two windows:

The upper pop-up window shows a 3D representation of the protein that can be rotated by holding down your computer mouse button and dragging. You can zoom in or out under the “View” menu.  This default representation displays a helices as green cylinders, b sheets in gold, and loops in blue.  From the menu at the top, you can open the drop down menu under “Style”, select “Rendering Shortcuts”, and change the type of representation of the amino acid chain.  You can also select “Toggle Sidechains” at the bottom of that menu to see both secondary structure and the R-groups.

The lower pop-up window shows the primary sequence of the two amino acid chains or subunits that make up this protein. The amino acid residues are indicated by their one letter abbreviation, which is color-coded to match the representations in the 3D viewer.  If you click and highlight amino acid residues in the linear sequence, the amino acids will be highlighted in the structural representation as well.

Frequently Asked Questions:

How do I copy information from the structural display into a report? 
For a PC, try using the steps outlined below (For a Mac, try the Grab program):

1. When you have the image you want on your screen, press Alt+PrintScrn at the same time.  

2. Open the Paint program.

3. Use the “paste” command to place your screen shot into Paint.

4. Select regions you want to cut and paste.

Additional molecular modeling database help and conserved domains and protein classification help is provided on the Structure website.