All-atom molecular dynamics trajectories of the trimeric CD27-CD70 complex and its N88A mutant

All-atom molecular dynamics trajectories of the trimeric CD27-CD70 complex, comprising four independent replicates of each the wildtype and the N88A mutant, in which N88 is substituted by alanine in all three CD27 monomers. Complexes were built from the PDB ID 7KX0, the hexameric assembly of an inner CD70 trimer and an outer CD27 trimer, with the resolved N-linked glycans retained, solvated in TIP3P water at 150 mM potassium chloride concentration and parameterized with the CHARMM36m force field. Each replicate was propagated for 2.25 microseconds in OpenMM 8.0 employing a Langevin integrator at 300 K, a 2 femtosecond timestep, and particle mesh Ewald electrostatics with a 1.0 nanometre cutoff. The total sampling is 18 microseconds. Trajectories are deposited with water removed, and coordinates are imaged at 11250 frames per replicate, written every 200 picoseconds, together with the corresponding topologies in PDB format.