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The glycosaminoglycans are covalently bound to core protein to form aggrecan in a structure that locates keratan sulfate side arms preferentially close to the linkage region to hyaluronan. The keratan sulfate molecules characteristically are of lower molecular weight than the chondroitin sulfate chains.

The core protein molecule has three globular domains, called G1, G2, and G3. The G1 region is the point of attachment of proteoglycan to hyaluronan to create aggregate, G2 is located near the keratan sulfate rich region, and G3 is located at the opposite terminal end of the core protein. Phosphorylation of serine residues occurs adjacent to the chondroitin sulfate–containing peptides of the core protein.

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