Kiwifruit metallothionein, kiwi503, is a typical plant metallothionein protein. It has 63 amino acid residues in two cysteine-rich regions and one spacer region of about 32 residues. In this note, the two cysteine-rich regions and the spacer region have been modeled separately by the distance geometry and the homology method. The three parts are then connected to generate a three-dimensional structural model of kiwifruit metallothionein kiwi503. The result shows that there is no structural or energy barrier preventing either cysteine rich domain from independently forming a metal-sulfur chelating cluster. The method can also be applied to predicting the structures of the same type of other proteins.