Launch guide window

Launch NCBI Home Page

Goals

• Find information about heterogens from a PDB file
• Find an amino acid pattern in a protein sequence
• Display a side chain for a residue in the pattern
• Create a custom annotation of the heterogen binding site

Steps

1. Find a structure record using Entrez
   
   • On the NCBI home page, choose Structure from the Search menu.
   • Enter PDB code 2NOS and click Go.

2. Identify heterogens in the structure
   
   • Click on the accession number, 2NOS, to open the structure summary page.
   • Scroll down to the bottom of the page. What heterogen groups are linked to this record?
   • When was this structure deposited?

3. View the structure in Cn3D
   
   • Click the structure image on the structure summary page.

4. Find an amino acid pattern
   
   • In the Sequence/Alignment Viewer, choose View / Find Pattern.
   • Search for the nitric oxide synthase (NOS) signature, RCIGRIQW, in which the cysteine is the heme iron ligand.

5. Select a single residue in the pattern
   
   • Find the (yellow) highlighted amino acids in the structure window.
   • Highlight only the cysteine in the pattern by clicking on it in the sequence viewer.

6. Create a custom annotation
   
   • In the structure window, choose Style / Annotate.
   • Click "New" and enter a name for the annotation.
   • Click "Edit Style" and uncheck the boxes next to Helix Objects and Strand Objects.

7. Display and label the side chains
   
   • Check the box next to protein side chains, and render them as "Tubes" using a color of your choice.
   • Click the Labels tab, and set the spacing to 1 under Protein Backbone.
   • Click Done, then OK, and Done.

8. View your annotation
   
   • In the structure, double click on the heterogen, protoporphyrin IX containing Fe.
   • Choose Show/Hide / Show Selected Residues.
   • Click in any white space in the sequence window to remove the highlighting.

9. Save your work
   You can now save the annotated file for future use.

Revised December 3, 2007