Kinesin

PDB file 3KIN

This file depicts the crystal structure of the dimeric head & neck domains of rat brain kinesin. This structure was published by F. Kozielski, S. Sack, A. Marx, M. Thormahlen, E. Schonbrunn, V. Biou, A. Thompson, E. M. Mandelkow and E. Mandelkow in 1997. The bound nucleotide is ADP. 

Suggested display options:

Color chain and display as cartoon.
View also with color structure to emphasize the secondary structure.
Look for the coiled coil of the truncated neck domain.

Select hetero-ligand, display as spacefill, and color CPK.
Note that the nucleotide binding pocket is formed by loops extending from a b-sheet, as in proteins of the Ras superfamily.

Select 232-237 and display as ball & stick or spacefill with color CPK, to visualize the position of a loop (sequence Asp-Leu-Ala-Gly-Ser-Glu) that is part of a domain designated switch II.
This loop, which is adjacent to the ADP phosphates, undergoes a significant shift in position depending on what is occupying the nucleotide binding site. A partly homologous switch region is found at this location also in myosin.

Locate the conserved glycine (residue 235) which is thought to be particularly important in sensing the presence or absence of the terminal phosphate of a bound nucleotide.

Question: Do the two head domains have equivalent orientations relative to the coiled coil neck domain?

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