PDB file 1AVD
This structure of hen egg-white avidin, complexed with biotin, was determined by L. Pugliese A. Coda, M. Malcovati, & M. Bolognesi in 1994.
Suggested display options:
1. Color chain to
distinguish the 2 copies of the protein.
Display as cartoon.
What is the major secondary structure of avidin?
2. To visualize the biotin, select
residue-btn, display as
ball & sticks and color CPK.
Where is biotin located relative to the protein?
Note that if you select "ligand" an N-acetyl-glucosamine (a common protein glycosylation) is also selected.
3. A disulfide linkage ties together one end of the barrel.
Visualize this by selecting residue-cys, display as sticks, and color CPK so you can distinguish the yellow sulfurs.
Also try displaying these in spacefill.
4. Select protein and convert to
Then select protein-sidechain and display as spacefill.
Separately select protein - hydrophobic and polar, and give each a color.
What type of amino acid predominantly fills the interior of the b barrel?
Try positioning with one avidin end-on and then choose options-slab mode. Left drag while holding down the control key.
Or press Back button
at top twice
to return to your place in the notes.