The shape of a protein molecule is determined completely by

Its primary structure.

Explanation:

Proteins is polymers of the alpha amino acids that are linked together through the peptide bond. Proteins acts as the main building block of the body.

Proteins works effectively at its 3D shape. The shape of the protein is determined by the primary structure of the protein. The primary structure includes the sequence of the amino acids that determines the shape, structure and function of protein.

Thus, the answer is primary structure.