Binding pocket superposition

Fig. 9 Best-fit superposition of CORCEMA-ST optimized structure (red) with the energy-minimized crystal structure (protein residues within the binding pocket are black and ligand residues are green). The hydrogens were omitted for clarity. Reprinted with permission from [70] 2005, American Chemical Society...

As regards the first four molecules (those supposed to interact most similarly with the binding pocket), two basic alignments were identified. In both, colchicine, allocolchicine and MTC overlapped in a similar fashion, whereas combretastatin assumed two different orientations. In the first superposition, considered more likely... 

Figure 2. Superposition of the coenzyme binding pockets of IMDH (light gray) with NAD (middle gray) and IDH (black) with NADP (dark gray with the 2 -phosphate in black). Dashes indicate H-bonds. IMDH numbering is used throughout, except in the a-helix and loop of IDH where IDH numbering is italicized.

Fig. 7.12 Photoisomerization in rhodopsin. Superposition of the chromophore structure in the protein binding pocket in the dark state (black), at the Sj-Sq transition (red), and after 500 fs of relaxation in the isomerized state (green).

Fig. 10 Fructose superimposed on mannose in the FimH binding pocket. Fructose in green (for clarity of the picture, each atom was shifted 0.3 A from the ideal superposition), mannose in grey. The two different Tyr48 side chain conformations are shown. Note the lack of 01 of mannose (anomeric oxygen) and the presence of (an extra) hydroxyl on C2 (the equivalent of C5 of mannose) that is in close contact (2.7 A) with Ile52 (orange dashed bond)...

Fig. 9. rhe carotenoids. Superposition of the spheroidene and 1,2-dihydroneurosporene molecules from Rb. sphaeroides (shown in Color Plate 9 in red) and Rp. viridis (shown in Color Plate 9 in green) RC. The binding pocket is formed by six (three) phenylalanines and five (two) tryptophans in the Rb. sphaeroides (Rp. viridis) RC. Upper View perpendicular to the planes of the carotenoids. Lower View rotated by 90°. (See also Color Plate 9)... 

Superposition of the active site of COX-1 (yellow) with COX-2 (purple) and the COX-2-selective inhibitor SC-558. The larger NSAID binding pocket is clearly visible. The access to this side-pocket is more restricted In COX- 7 because of the larger iso-leucine Instead of valine-523. 

Figure 7.14 The superposition of the free-state enzyme structure and the complex structure on the residues coordinated with catalytic zinc ion. It is shown that the substrate-binding pocket of the free-state enzyme served as an open state, whUe the complex served as a closed state . The conformation of the labeled residues changed significantly to make the substrate analog binding more stable in the complex structure. 2007 Elsevier Ltd.

Fig. 10.4. HsIVU activation mechanism. (A) Stereo view (C -trace) of the superposition of the C-domain of an HsIU subunit (red) from the original E. coli HsIVU complex onto that of the H. influenzae HsIU subunit (green) from its complex Two HsIV subunits (pink and blue) from the H. influenzae complex are also shown to illustrate the binding of the C-terminal segment of H. influenzae HsIU to the pocket between the HsIV subunits (indicated also by a...

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