Zellweger syndrome is an autosomal recessive disorder caused by mutations in genes that encode peroxins, proteins required for the normal assembly of peroxisomes. It causes a defect is the perioxisomes, which affects the body severally. It affects both males and females and is present at birth. The target gene coding protein in zellweger syndrome had been identified. Blast P is used for the similarities identification of pxr1 protein and the Functional identification of pxr1 is viewed through AMIGO. Secondary structural analyses of pxr1 protein were carried through tools like, TARGET P, GLOBPROT and DOMAIN LINKER PREDICTION. From the molecular mechanics study, the electrostatic properties have been identified.