The ability of X-ray crystallography to provide accurate information about macromolecular structures, including the molecular
details of the interactions between proteins and small
molecules, is unsurpassed. However, one has to remember that a crystal structure is merely
a “snapshot” representing an "average macromolecule". In addition, there are other limitations of
X-ray crystallography that can significantly affect our interpretation of biochemical or biological
processes. Such limitations will be discussed in the examples provided by analysis of
pathogenesis-related class 10 protein (PR-10) originating from peanuts. The PR-10 protein,
which is also a minor peanut allergen (Ara h 8), has an unusually large binding cavity and
functions as a small molecule carrier. Conformational changes and the large ligand-binding
cavity allow the protein to bind molecules that significantly differ in their structure. For example,
we were able to demonstrate that the protein binds flavonoids, steroids, fatty acids and some
plant hormones like zeatin. It is also possible that the ligand binding affects the immunological
properties of PR-10 related allergens.