Fig. 4: Structural analysis of the KITbp-KIT complex.
From: Improved protein binder design using β-pairing targeted RFdiffusion
a Crystal structure (PDB ID: 9H71) of KITbp (cyan) in complex with KIT (green) and 2Fo-Fc electron density contoured at +1.0 RMSD (gold). b The KITbp crystal structure superimposes on the binder design model (grey) with subangstrom backbone atom RMSD, and 2.0 Å all-atom RMSD. c Close-up views of the binder interface reveal high shape complementarity of the binder-target complex (top). The binder interface consists of hydrophobic and polar interactions between binder core-boundary residues and KIT receptor domain 2 core-boundary residues (middle). The binder forms an extensive hydrogen-bond β-pairing interaction with the targeted domain 2 edge strand (bottom). There are multiple side-chain interactions between binder and KIT tyrosine residues (Y38 and Y39 in the binder; Y259 and Y269 in KIT) in the core-boundary interaction, and between binder glutamate residues (E14, E28, E24, E35) and KIT hydrogen bond donors (Q256, K258, N260, W262, H263, R271). The binder also makes electrostatic interactions with both the opposite domain 2 edge strand and KIT domain 3. Source data are provided as a Source Data file.
