On the NCBI home page, enter the following query into the search box and click Go:
dna photolyase AND thermus thermophilus[organism]
Click on the number of Structure hits to view them
Open the Structure Summary page
Click on the accession of the record that is not a complex, 1IQR.
View the structure in Cn3D
Click the structure image to launch Cn3D.
Locate a bound co-factor
In the structure window, choose Style / Coloring Shortcuts / Molecule.
Find the bound FAD co-factor. It will appear as
a brown "ball and sticks" model in the middle of the structure.
Select the co-factor
Zoom in on the FAD co-factor, and double click on any atom of the FAD to highlight it. It will turn yellow when you have succeeded.
Find residues within 3 Angstroms of the FAD
In the structure window, choose Show/Hide / Select by Distance / Residues only.
Enter a radius of 3.0 Angstroms in the box. Click OK.
All residues within 3.0 angstroms of the FAD should now be highlighted in yellow.
Create a custom annotation
In the structure window, choose Style / Annotate.
Click "New" and enter a name for the annotation.
Annotate side chains
Click "Edit Style" and uncheck the boxes next to Helix Objects and
Strand Objects.
Check the box next to Protein sidechains, and choose a rendering style and color
of your choice from the menus to the right.
Annotate and label the backbone
Select Tubes from the rendering menu next to protein backbone, and then select
Complete under Show. Color the backbone as you like.
Click on the Labels tab, and set the spacing to 1 under Protein Backbone, and select one-letter type.
Click Done, then OK, and Done.
Display your annotation
In the structure window, choose Show/Hide / Show Selected Residues.
If you still see helix or strand objects, choose Style / Edit Global Style and
uncheck the boxes for Helix Object and Strand Object.
Click anywhere in the sequence window to remove the highlighting.
Save your work
You can now use File / Save As to save the annotated file for future use.
