Here is an example on how to superimpose the structures of two proteins and display the sequence conservation around the ligand binding pocket.

PDB Search

• PDB Search Tab 1ql6
• PDB Search Tab 1ian

• Select both receptors by double clicking on the name of the receptor in the ICM Workspace. To select two receptors use the Ctrl button or use the shift button to select a range of objects in the ICM Workspace. A receptor which is selected will be highlighted in blue in the ICM Workspace and with green crosses in the graphical display.

• Superimpose both structures by clicking on the display tab and selecting the superimpose button.

• Now that the structures are superimposed we can unselect everything - to do this right click and drag in blank space in the graphical display or double click in white space in the ICM Workspace or use the unselect button green box with red cross through it.
• Now extract the sequence information from each protein. To do this right click on the molecule "a" of 1ql6 and molecule "m" of 1ian. and select extract sequences. Once the sequences have been extracted you should see the sequence in the ICM Workspace entitled 1ql6_a and 1ian_m

• Now align the sequences by selecting both sequences right clicking and selecting Align sequences. An alignment will be displayed at the bottom of the graphical user interface.
• Next we need to select the ligand ATP and select a sphere of residues around the ligand. To do this double click on the ATP molecule in 1ql6 (batp) in the ICM Workspace. You should see green crosses in the graphical display. Right click on the ATP molecule in the ICM Workspace and select neighbors. Enter a value of 6A for the radius. Select all_objects for the type of selection. Click ok and you should see a cluster of green crosses in the two proteins around the ligand and selected residues will be highlighted in blue in the alignment.

• Right click in white space in the alignment and select display tools panel.
• In the alignment tools panel select propogate to all sequences.
• Select the "invert" button to invert the current selection.
• Select the "hide" button to hide the current selection and you will be left with the residues surrounding the binding pocket in the alignment.

NOTE: Please note that all alignments are linked with structure therefore selections can be made in the alignment. Also as an example structure can be colored according to the color in the alignment which is useful for identifying conserved regions.