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.
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.
Return to
Lecture Notes
on Gluconeogenesis
Or press Back button
at top twice
to return to your place in the notes.