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. 2016 May 23;291(29):15156–15168. doi: 10.1074/jbc.M116.732503

FIGURE 3.

FIGURE 3.

Crystal structure of the uPA-Nb4 complex. a, interaction of Nb4 (orange) with uPA (green) is primarily mediated by the CDR-H3, which interacts in a substrate-like manner with the substrate-binding pockets in the active site region of uPA (S4-S3′). The Nb4-uPA interaction surface is colored light blue. b, enlarged view of the P1-S1 interactions. The P1 Arg-110 of Nb4 (orange) inserts into the S1 pocket of uPA (green) to form interactions with Asp-189 at the bottom of the pocket. The carbonyl oxygen atom of Arg-110 is aligned in a substrate-like manner in the oxyanion hole, and the distance from the oxygen atom of the catalytic Ser-195 in uPA to the P1 carbonyl group in Nb4 is 2.8 Å (indicated in red). c, exosite interactions between the CDR-H1 of Nb4 (orange) and the 37s loop of uPA (green). Polar interactions are indicated as black dashed lines.