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Figure 2.
FIGURE 2. Superposition of all LiPDF structures. A, all
observed conformational states of LiPDF are superimposed to
reveal the differences around the substrate pocket. Pink, closed
state at pH 3.0; brown, all closed states within pH values
6.5-8.0; blue, half-open state; cyan, open state at pH 3.0.
Residues Tyr^72 and Arg^109 (ball-and-stick model) undergo
significant conformational change during the conversion between
different states. The competitive inhibitor actinonin (black),
which was bound to the half-open state (blue) would collide with
the pocket in the closed states. With the opening of the
substrate pocket, the side chain of Arg^109 swung up toward the
molecular surface. Compared with the closed state at pH 3.0, the
closed states within the pH range 6.5-8.0 displayed a slightly
open pocket. B, a schematic is shown to help compare these
different states. The color scheme is consistent in both panels.
This figure was prepared using Molscript (30) and Raster3D (31).
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