Pdr1p and Pdr3p is a part of Gal4 transcription factor family due to their zinc-finger DNA binding motif, which is located in N-terminus end of Pdr1p. Pdr1p also contains a long internal region of many inhibitory domains and possess a C-terminal transcription activation domain (amino acids 879–1036). The transcriptional activation domain is rich in glutamine and asparagine, which is theorized to facilitate in protein-protein interaction via  hydrogen bonding. A study found that DNA-binding domain of Pdr1p was sufficient for recognizing its endogenous target genes.  Strong drug resistance phenotype of yeasts with pdr1-3 is speculated due to its inability to bind to ligands that otherwise cause conformational change to inhibit the transcriptional activity of Pdr1p.