The structure of the Strepavidin-biotin complex was determined by Weber et al. [Science 243:85, 1989, but also see Weber et al., J. Am. Chem. Soc. 114:3197, 1992]. Each of the four identical chains has 159 amino acids. The atomic coordinates of amino acids 13-133 (molecules with chains going from residues 13 - 138 bind biotin with full affinity) are deposited in the Brookhaven Data Base <http://www.pdb.bnl.gov> as pdb files.
Most molecular viewing programs can read and display information from pdb files, including the freeware RasMol, written by Roger Sayle [email@example.com] at Glaxo Research and Development. We have used this program to produce the following ribbon representation of the polypeptide backbone, in order to show the overall structure of the protein. In yellow are five segments of one beta sheet and three segments of another. The chains of the two sheets are at 90 degrees to each other, but the sheets are parallel. There are two small alpha helixes in pink. The bound biotin is not visible here.
The next picture is the same structure in the same orientation, but produced by the freeware program SwissPdbViewer written by Nicolas Guex. It can be obtained at the pdb site given earlier: <http://www.pdb.bnl.gov/expasy/spdbv/mainpage.html>
Now the individual amino acids are visible, and the bound biotin is seen in green. The binding pocket for biotin is in a deep cleft, and it is not hard to believe (although it isn't seen here directly) that there are many points of contact between biotin and the protein that are responsible for the high affinity between the two molecules.