Avidin-Biotin

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 wireframe.
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.


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