Obtain the PDB file with code 2iff (see section 1 if you need a reminder about how to get a PDB file.). After the file appears on the desktop, rename it 2iff.pdb. Then drag it onto the RasMac v2.6 icon to open it. For sections 8 and 9 of this tutorial, you must make sure that you are using the desktop copy of RasMol; otherwise you may have difficulty finding files that you create using RasMol.
The file 2iff.pdb is larger than 3b5c.pdb and takes longer to load. When loading is complete, RasMol provides some information about the file in the Command Window, and shows a complete wireframe model in the Main Window. Arrange the windows as described in section 1. Move the model around to get some feeling for its size and complexity in comparison to cytochrome b5.
Display: Backbone
Colours: Chain
RasMol presents each chain in a different color. This allow you
to see immediately how many different chains are present. Click on
any atom in the pea-green chain. (the smaller of the two chains shown
in shades of green). On the command line, RasMol displays something
like
Atom: CA 2574 Group: GLY 117 Chain: Y
This tells you that the green chain is designated Y in the PDB file. With oligomeric proteins, you need to know chain designation in order to compose specific select and restrict commands. Other than the need for chain designations, exploring a multi-chain model is just like exploring a single chain. Identify the other chains by clicking on them. Chain Y is the enzyme lysozyme from hen egg white. Chains H and L are the antigen-binding parts of the heavy chain and light chain of a mouse antibody. Together, they are called an Fab fragment. The antibody was made by immunizing a mouse with hen lysozyme and then purifying a specific antibody to lysozyme So in this model, lysozyme is the antigen.
RasMol > select helix or sheet <
return >
Display: Cartoons
Colours: Structure
The first command selects all residues that are in either alpha
helical or beta pleated sheet conformations. (The command select
helix and sheet selects nothing. Why?) The Display
and Colours commands affect only the selected residues, so the
non-helical and non-sheet portions remain in colors that allow you to
distinguish them as separate chains. You can see that the antigen (Y)
contains several alpha helices and a 3-strand pleated sheet, and that
the antibody chains are primarily beta structure. The two antibody
chains each exhibit two domains of the immunoglobulin
fold, a beta structure that is found in all antibodies, as
well as some other proteins whose function is recognition.
RasMol > select :H or :L < return
>
Display: Backbone
Colours: Chain
RasMol > select within (6.5, :Y) and not :Y < return
>
RasMol > color white < return >
Parts of the antibody backbone that are close enough to the antigen
to be involved in the antigen-antibody interaction are now shown in
white. With a few commands, you have focused on what are called the
"complementarity determining regions" (CDRs) of the antibody. By
restricting your display to these regions and adding all atoms in
wireframe, you could explore in detail the interactions that bind
this antibody to its antigen.
Now go directly to the next section of the tutorial. You will learn how to save and recover the view you have just created.