1. An apparatus for comparing a protein structure using a three-dimensional relative directional angle (3D RDA) and a Fourier descriptor, comprising: a 3D RDA coder configured to code a 3D RDA of a target protein data or an inquiry protein data inputted from the outside; a Fourier transformer configured to obtain Fourier coefficients by Fourier transforming 3D RDA coding values coded by the 3D RDA coder; a comparator configured to compare the obtained Fourier coefficient of the target protein data with the obtained Fourier coefficient of the inquiry protein data; and a data generator configured to output protein data in order from high similarity to low similarity according to the comparison result of the comparator.