STEP ONE: Searching the PDB Database

• Select the pdb search tab and enter the search string kinase. A table will be displayed with your search results.
• In this example we will view the PDB code 2BDW. The easiest way to find 2BDW in the table is to sort the table by ID. You can do this by right clicking on the column header ID and select Sort or another way is to right click on the table and select Find in Table.
• Double click on the row and the kinase structure will be displayed.

STEP TWO: Coloring, Structural Representation and Annotation

If you look in the ICM Workspace (left hand side of the screen) you will see that this structure consists of two chains a and b. We can color the structure by individual chains by:

• Select the display tab.
• Click and hold on the ribbon display button and select color by-> and choose molecule. The individual chains a and b will be colored as shown below.

Now let us display the two residues involved in making a key activation salt bridge (Glu60 and Lys42). For clarity we will only work with the "a" subunit so first we will delete the "b" subunit and water molecules

• In the ICM Workspace double click on "b" whilst holding the CTRL button and then double click on "W" (water). Selected regions will be highlighted in blue in the ICM Worksapce and green crosses in the graphical display.
• Right click on the molecules and select Delete.

Now we will select Lys42 and Glu60 and display in xstick representation

• Expand the sequence information relating to subunit "a" as shown below.
• Select the residues by clicking over them and dragging. They will be highlighted blue in the ICM Workspace when selected. You can select both residues at the same time by holding the CTRL button.
• Now click on the xstick representation button

Now we will annotate this selection.

• Right click on one of the residues and select annotate selection
• Add annotation as shown below.

STEP THREE: Making a molecular document

The view of the salt bridge will constitute our first SLIDE to add to a molecular document.

To make the slide:

• Click on the Slide button (Camera)

To make the text portion of a molecular document:

• File/New HTML
• Add some text and click OK
• Right click on the text window and select Edit Source
• Highlight the text you wish to link to the first slide and select the camera button in the editor.
• Select the slide from the drop down menu.

Try adding other annotation and transitions as shown below.