Start SPDBV

Does Magic fit work?

For both structures Display the CA backbone only and color according to secondary structure. Use the layer info panel and orient the two structures so that they look similar.

Select the ADP molecules only

Use the 3 point alignment approach to align the ADP molecules

make the whole molecules visible again

move one structure over to the right (no turning)

select the ADP molecules

In the control panel header click on the cloud icon to display both ADPs in space filling mode.

In display click on render Q3D.

 

(To get more spectacular displays, you can save the pictures as POV files and use the program POV ray to make even nicer images)

 

If you have time, do the same for 1GSA, 2DLN and CPSBfrag and CPSFfrag. The latter two files are clippings of the front and back ATP binding sites of the carbamoyl phosphate synthetase (1BXR).

 

WHAT DOES THIS MEAN? Recall the use of 2DLN in PSI blast. Are all of these structures homologues? What does that tell you about evolution of proteins? An illustration is here.