PDB file 1ICM
This file depicts intestinal fatty acid binding protein, co-crystallized with bound myristate, a 14-C fatty acid. The structure was solved by J. C. Eads, J. C. Sacchettini, A. Kromminga, & J. I Gordon in 1993.
Suggested display options:
Display the protein as cartoon with color structure, to visualize the b-strands.
Note the "b-clam" structure, consisting of 2 approximately orthoganal b-sheets, enclosing a cavity.
To visualize the fatty acid, select
hetero-ligand, color CPK, and display as ball &
stick or spacefill.
Note the position of the fatty acid within the b-clam.
Select water, display as ball and stick, and specify a color. Rotate to see that some
water molecules are within the interior.
Type in select HOH170, display as spacefill, and note the proximity of this water that forms a H-bond with the carboxyl group of the fatty acid.
Select protein and change the display to wireframe with color CPK.
Question: What positively charged amino acid has its sidechain nitrogen atoms adjacent to the carboxyl group of the fatty acid?
The interior is not totally hydrophobic, but there
are inward-facing hydrophobic residues that interact with the fatty acid tail.
Identify some of these.
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