Background When inspecting a ligand binding pocket it is important to check that the true pocket is formed by chains which are not explicitely present in a PDB entry. Therefore it is necesary to use Tools/Crystallographic Neighbor to find all molecules/subunits or chains involved in the interaction with the ligand. Molecular objects and 3D density maps may contain information about crystallographic symmetry. It consists of the following parameters:

1. Crystallographic group eg. P2121 that determine N (depends on a group) transformations for the atoms in the asymetric unit.
2. Crystallographic cell parameters A, B, C, Alpha, Beta and Gamma

Example As an example let us look at Cycloldextrin glycosyltransferase (PDB Code: 1CDG). The problem with docking to this receptor is that the true pocket is formed by chains which are not explicitly present in the PDB entry. Site mb1 includes serine 382. This cannot be predicted just by looking at the structure. Therefore we need to identify symmetry related molecules to this protein.

• Use the PDB search tab to load the crystal structure 1cdg.
• Inspect the ligand binding pocket of maltose (mal)
• To identify if there are any other chains involved in the interaction with the ligand select the whole structure in the ICM Workspace.

• Tools/Crystallographic Neighbor
• Select a 7A radius
• Check "create symmetry related molecules" and "display symmetry neighbors".
• Inspect the neighbors surrounding maltose(mal). Each symmetry related subunit can be colored by object by clicking and holding the representation button in the display tab and selecting color-by.