Figure 3
Figure 3. The binding pocket of RUC-1 in the closed αIIbβ3 headpiece crystal structure. (A) Overview of RUC-1 binding site. αIIb (light blue), β3 (wheat), and Fab (gray) are shown as solvent-accessible surfaces. RUC-1 is shown as spheres with green carbons, red oxygens, blue nitrogens, and yellow sulfurs. (B) Close-up of the RUC-1 binding site. Selected side chain and backbone atoms are shown in stick with other regions in cartoon. Color code is as in panel A. A simulated annealing omit map for RUC-1 is shown at 1σ. Water molecules are small red spheres. (C) The tirofiban binding site (Protein Data Bank code 2VDM). Color code is same as in panel A. Ca2+ ions of the SyMBS or the ADMIDAS (yellow), and the Mg2+ ion of MIDAS (silver) are shown as spheres. (D, F, and G) Comparison of RUC-1, KQAGDV, and RGDV binding sites. Color codes are as above, except KQAGDV and RGDV are shown as sticks with cyan carbons, after superposition on the RUC-1 complex using super command in Pymol with the αIIb β-propeller and β3 βI domains. (E) Comparison of small molecule binding locations. Crystal structures (Protein Data Bank code in parentheses) containing the indicated small molecules were superimposed as above. The ligands from the structures are shown in exactly the same alignment, except for vertical separation on the page.

The binding pocket of RUC-1 in the closed αIIbβ3 headpiece crystal structure. (A) Overview of RUC-1 binding site. αIIb (light blue), β3 (wheat), and Fab (gray) are shown as solvent-accessible surfaces. RUC-1 is shown as spheres with green carbons, red oxygens, blue nitrogens, and yellow sulfurs. (B) Close-up of the RUC-1 binding site. Selected side chain and backbone atoms are shown in stick with other regions in cartoon. Color code is as in panel A. A simulated annealing omit map for RUC-1 is shown at 1σ. Water molecules are small red spheres. (C) The tirofiban binding site (Protein Data Bank code 2VDM). Color code is same as in panel A. Ca2+ ions of the SyMBS or the ADMIDAS (yellow), and the Mg2+ ion of MIDAS (silver) are shown as spheres. (D, F, and G) Comparison of RUC-1, KQAGDV, and RGDV binding sites. Color codes are as above, except KQAGDV and RGDV are shown as sticks with cyan carbons, after superposition on the RUC-1 complex using super command in Pymol with the αIIb β-propeller and β3 βI domains. (E) Comparison of small molecule binding locations. Crystal structures (Protein Data Bank code in parentheses) containing the indicated small molecules were superimposed as above. The ligands from the structures are shown in exactly the same alignment, except for vertical separation on the page.

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