Info

NA = not available, although paper describing the structure has been reported. Blank in the uncomplexed column means structure has not been reported.

"Antibodies are Fabs unless noted as Fv.

"Antigen names: HPr, histidine-containing protein of the phosphoenolpyruvate:sugar phosphotransferase system; FMDV, foot-and-mouth disease virus; TEMPO-DNP, 2,2,6,6,-tetramethyl-1-piperindinyloxy dinitrophenol; EOTUBE, 4-[W'-(2-hydroxyethyl)thioureido]-L-benzyl-EDTA; NC174, /V-(p-cyanophenyl)-A/'-(diphenylmethyl)-/V"-(carboxymethyl)guanidine.

NA = not available, although paper describing the structure has been reported. Blank in the uncomplexed column means structure has not been reported.

"Antibodies are Fabs unless noted as Fv.

"Antigen names: HPr, histidine-containing protein of the phosphoenolpyruvate:sugar phosphotransferase system; FMDV, foot-and-mouth disease virus; TEMPO-DNP, 2,2,6,6,-tetramethyl-1-piperindinyloxy dinitrophenol; EOTUBE, 4-[W'-(2-hydroxyethyl)thioureido]-L-benzyl-EDTA; NC174, /V-(p-cyanophenyl)-A/'-(diphenylmethyl)-/V"-(carboxymethyl)guanidine.

Figure 1 Binding sites and buried surfaces (represented as dots) of selected antibody-antigen complexes demonstrating different sizes and shapes of binding interfaces. For each complex, on the left the antibodies are shown with antigen-binding site face-on and on the right rotated 90° about the horizontal relative to the figure on the left. In both views the light chain is on the left. In the right image, the viewer is looking from CDR-L3 towards CDR-H3, which is in the back. Antibody backbone is represented as a ribbon. To the far left and far right of the antibody structures the small molecule antigens for the first three complexes are represented as ball-and-stick in the orientation that they are bound to the antibody. (A) 26-10-digoxin; (B) BR96-Lewis Y; (C) 50.1-HIV gp120 V3; (D) HyHEL-5-lysozyme. Note the deep pocket of 26-10, the broad pocket of BR96, the groove of 50.1 and the relatively flat and extensive surface of HyHEL-5. (Figure produced with MOLSCRIPT by Per Kraulis.)

large hydrophobic surfaces. Moreover, these large hydrophobic surfaces can be immobilized with limited entropy loss due to restricted rotation of bonds in the complex. Thus the preference for tyrosines and tryptophans is most likely due to the unique nature of the antigen-binding site, which spends part of its time accessible to solvent and part of its time buried in a complex.

the limited number of structures of uncomplexed antibody available for protein-specific antibodies (Table 1). An example of rotation of VH relative to VL and of conformational rearrangement of the third CDR of the heavy chain may be seen in Figure 2A. The effects of these motions on opening the antigen-binding site may be seen by a comparison of Figure 2B with Figure 2C.

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