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Volume 9, Issue 10, Pages 887-895 (October 2001) Structural Basis of HIV-1 and HIV-2 Protease Inhibition by a Monoclonal Antibody Pavlina Rezacova, Julien Lescar, Jiri Brynda, Milan Fabry, Magda Horejsi, Juraj Sedlacek, Graham A. Bentley Structure Volume 9, Issue 10, Pages 887-895 (October 2001) DOI: 10.1016/S0969-2126(01)00654-2

Figure 1 Inhibition of HIV-1 Pr and HIV-2 Pr Activity by scFv1696 (a) The inhibition of HIV-1 Pr activity. (b) The inhibition of HIV-2 Pr activity. The initial reaction velocity (vi) of HIV-1 Pr and HIV-2 Pr, normalized to the initial reaction velocity in the absence of scFv1696 (v0), is plotted as a function of scFv1696 concentration. The curves show the best fit of the tight binding model [13] to the experimental data (see text for details) Structure 2001 9, 887-895DOI: (10.1016/S0969-2126(01)00654-2)

Figure 2 Stereo View from above the Antigen Binding Site An omit-electron density map calculated with coefficients (Fo-Fc) and phases from the refined model without the peptide residues, contoured at 2.5 rms level. The VH domain is in red, the VL domain is in violet, and the peptide and solvent molecules are in green Structure 2001 9, 887-895DOI: (10.1016/S0969-2126(01)00654-2)

Figure 3 Schematic View of the scFv1696-Peptide Complex All scFv1696 residues in contact with the peptide are indicated Structure 2001 9, 887-895DOI: (10.1016/S0969-2126(01)00654-2)

Figure 4 Comparison of the Variable Domains of Noncomplexed Fab1696, PDB Entry 1c17, with the scFv1696 Peptide Complex (a) A side view. (b) Viewed from above the antigen binding site. The noncomplexed state is shown in blue, the complexed state is shown in yellow, and the peptide is shown in red. Superpositions were made by optimizing the correspondence between the VL domains Structure 2001 9, 887-895DOI: (10.1016/S0969-2126(01)00654-2)

Figure 5 An Overhead View of the Topology of the Antigen Binding Site (a) The nonliganded Fab1696 scFv1696 complex. (b) The liganded scFv1696 complex The surfaces are color coded for electrostatic potential in the range of −10 kBT(red) to +10 kBT (blue), where kB is the Boltzmann constant and T is the absolute temperature. This figure was prepared with GRASP [41] Structure 2001 9, 887-895DOI: (10.1016/S0969-2126(01)00654-2)

Figure 6 Comparison of the Structures Adopted by the Segment P1–P6 of HIV-1 Pr The complex with scFv1696 is shown in yellow, and in the native protease (PDB entry 3hvp), it is shown in red. The superposition was made by minimizing the rms difference in the main chain atomic positions of the P2–P5 segment (rms difference 1.2 Å) Structure 2001 9, 887-895DOI: (10.1016/S0969-2126(01)00654-2)