Protein 3D structure is one of the key factors in recognizing gene functions. The availability of protein structure data in Protein Data Bank (PDB) enables us to conduct gene function analysis. However, the molecules in the PDB, whose structures have been determined, are always not corresponding to a unique gene. That is to say, the mapping from gene to PDB is not one-to-one. Thus this uncertain property complicates the analysis and increases the difficulty of gene function analysis. In this paper, we attempt to tackle this challenging issue and we study the problem of predicting gene function from protein structures based on the gene-PDB mapping. We first obtain the gene-PDB mapping, which is important in representing a gene by the structure set of all its corresponding PDB molecules. We then define a new gene-gene similarity measurement based on the structure similarity between PDB molecules. We further show that this new measurement matches with gene functional similarity nicely. This means that the measurement we introduced here can be useful for gene function prediction. Numerical examples are given to demonstrate our claim.