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.
dentify some of these.

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