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Figure 5.
Figure 5. Comparison of Par-6 PDZ Domain in the Free and
Cdc42-Bound Forms(A) Ribbon overlay of the free (green) and
Cdc42 bound (orange) Par-6 PDZ domain. The root mean square
deviation (rmsd) between the free PDZ ensemble is shown compared
to the rmsd between the free ensemble and the Cdc42-bound
structure. The sequence of human Par-6B used for the crystal
structure is shown for comparison.(B) Comparison of the free and
Cdc42-bound Par-6 PDZ domains to other PDZ structures. Known PDZ
structures (black; PDB codes: 1BE9, 1G9O, 1GM1, 1I92, 1IHJ,
1KEF, 1KWA, 1PDR, 1QAU; only residues from the PDZ domains of
these structures are shown) have a tightly clustered
conformation that closely resembles the Cdc42-bound Par-6 PDZ
domain. The free Par-6 structure deviates from the canonical PDZ
fold, however. A statistical analysis of the conformational
differences between the free and Cdc42-bound Par-6 PDZ domains
and PSD-95 PDZ3 (PDB code 1BE9) is shown below the overlay.
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