In this paper, firstly, Alphafold2 was used to calculate the three-dimensional structure (predicting structure) of three proteins 2LY9, 6Y4F and 6YJ1, and compared with the protein structure (experimental structure) published by NCBI. Then, the quality of predicting structure was evaluated. The results showed that the RMSD values of the predicting structure were less than 3 Å, which was indicated that the difference distance between the predicted structure and the experimental structure was less than 0.3nm. TM score was higher than 0.5, which showed that the predicting structure by Alphafold2 had similar folding structure with the experimental structure. The ramachandran plot showed that the residues in most favoured regions [A,B,L], in additional allowed regions [a,b,l,p] and in generously allowed regions [~a,~b,~l,~p] was accounted for more than 90% of the whole number of non-glycine and non-proline residues. The above results showed that the function of predicting three-dimensional structure of protein by Alphafold2 was very highly accurate. Subsequently, Alphafold2 was used to predict the three-dimensional structure of protein related to auxin synthesis, and the stereo chemical quality of protein structure was checked through residue geometry and overall geometry. The ramachandran plot showed that the residues in most favoured regions [A,B,L], in additional allowed regions [a,b,l,p] and in generously allowed regions [~a,~b,~l,~p] was accounted for more than 90% of the whole number of non-glycine and non-proline residues. Therefore, the predicted structure by Alphafold2 could highly be as the experimental structure of protein.