Xanthan has a particularly complicated molecular structure. however the backbone of xanthan is a β-(1-4)-D-glucose which is the same as cellulose. Every alternate glucose reside has a three sugar side chain consisting of two mannose residues with a glucuronic acid residue between them. The mannose reside nearest the main chain can carry a C6 acetyl group and the terminal mannose can carry a pyruvate group between C4 and C6. The acetylation and pyruvylation levels vary depending on fermentation conditions but typical values. Typically pyruvate residues can be found on 30-40% of the terminal mannose residues whereas 60-70% of the internal mannose residues may contain acetate groups. Recent work has looked at the properties of GM modified strains of xanthan gum that are either deficient in acetate groups, pyruvate groups or both. (Talashek).
Xanthan is produced in its native state as a twin stranded, right handed five fold helix. The stability of the helix is strongly affected by the ionic environment. Upon heating the xanthan helix goes through a transition to a disordered state and upon cooling it reverts to a helical structure. However it is believed that native xanthan exists in a form where chains are paired and once that has been lost and the xanthan molecules allowed to reorder the exact pairing cannot be retained and a partially crosslinked structure is formed as helices twist around various neighbours.