MRGPRX2-allergen docking data: D184 salt bridge analysis of 11 protein allergens using HADDOCK3

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MRGPRX2 D184 engagement by food and pollen allergens: a computational hypothesis for IgE-independent mast-cell activation Docking coordinates, analysis tables, and figure-generating scripts for the manuscript "MRGPRX2 D184 engagement by food and pollen allergens: a computational hypothesis for IgE-independent mast-cell activation" (Suzuki et al., under peer review). This dataset contains HADDOCK3 protein-protein docking results for 11 clinically relevant protein allergens and 3 positive-control agonists docked against the MRGPRX2 receptor (PDB: 7VV6). Contents: (1) Strategy A docking coordinate PDB files for all clusters, (2) input ligand and receptor structures, (3) analysis tables (HADDOCK scores, D184 salt-bridge detection, inter-strategy agreement, in silico mutagenesis, negative-control docking, PRODIGY affinity, net-charge analysis), and (4) Python/PyMOL scripts for reproducing the figures. Version 2 (Revision 1, 2026): Adds the negative-control (decoy) docking experiment (ubiquitin, ribonuclease A, carbonic anhydrase II, maltose-binding protein), PRODIGY binding-affinity estimates, net-charge analysis (engagement tracks local Lys/Arg accessibility, not net charge), the unified cationic-N D184 criterion recomputation (Table S5, n=20 + pairwise kappa), and mature-chain Cry j 2 re-docking (reclassified LOW). Structure provenance corrected: Pru p 7 (PDB 8X67) and Cry j 7 (PDB 8X0R) are experimental NMR structures. Scripts included for reproduction.

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