The B3 DNA binding domain (DBD) is a highly conserved domain found exclusively in transcription factors (≥40 species) (Pfam PF02362) combined with other domains (InterPro: IPR003340).

It consists of 100-120 residues, includes seven beta strands and two alpha helices that form a DNA-binding pseudobarrel protein fold (SCOP 117343); it interacts with the major groove of DNA.

[1] In Arabidopsis thaliana, there are three main families of transcription factors that contain B3 domain:[2] PDB: 1WID​[1] and PDB: 1YEL​[8] are only known NMR solution phase structures of the B3 DNA Binding Domain.

The N-terminal domain of restriction endonuclease EcoRII; the C-terminal domain of restriction endonuclease BfiI possess a similar DNA-binding pseudobarrel protein fold.

[9][10]