Theory

It is very useful to know how a protein from the PDB may look in a biological environment. The PDB entries solved by X-ray crystallography and deposited in the PDB contain the information about the crystal structure rather than the biologically relevant structure. For example, for a viral capsid only one instance of capsid protein complex will be deposited and only one or two molecules of haemoglobin that is a tetramer in solution maybe deposited.

In some other cases the asymetric unit may contain more than one copy of a biologically monomeric protein. ICM reads the biological unit information and has a tool to generate a biological unit. Not every PDB entry has the biological unit information.

A gallery of images created using the ICM Biomolecule generator is shown below:

Left: PDB: 1DWN Bacteriophage Pp7 From Pseudomonas Aeruginosa At 3.7 A Resolution Right: PDB: 1C8E Feline Panleukopenia Virus Empty Capsid Structure At 3.0 A Resolution

Left: PDB: 1AL2 P1/Mahoney Poliovirus, Single Site Mutant V1160I At 2.9 A Resolution Right: PDB: 1LP3 Adeno-Associated Virus (Aav-2), A Vector For Human Gene Therapy At 3.0 A Resolution

NOTE: Right click on a PDB structure in the ICM workspace to determine whether a structure from the PDB has biological unit information. If it does have this information then there will be an option in the menu entitiled "Generate Biomolecules" if not the option will be blanked out.

To generate a biological unit with ICM:

• Select the object or PDB file.
• Select the menu Tools/Xray/Biomolecule Generator.

• Tick the makeAllBiomolecules box.
• Click OK - with very large molecules the biomolecule generation may take some time.