Objective

Here we will investigate the biological environment of a virus protein . PDB code 1DWN.

Background

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 asymmetric 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.

Instructions

• Read and load the PDB file 1DWN
• Tools/Xray/Biomolecule Generator
• Tick the makeAllBiomolecules box (Warning this may take a few minutes to generate)
• The generated molecules will be listed in the ICM Workspace. Each one can be selected and displayed.

Manual References (Web Links)

Biomolecule Generator