Birds use the magnetic field of the Earth to navigate during their annual migratory travel. The possible mechanism to explain the biophysics of this compass sense involves electron transfers within the photoreceptive protein cryptochrome. The magnetoreceptive functioning of cryptochromes is supposedly facilitated through an iron rich polymer complex which couples to multiple cryptochromes. The present investigation aims to independently reconstruct this complex and describe its interaction with Drosophila melanogaster cryptochromes. The polymer complex consists of ISCA1 protein monomers with internally bound iron sulphur clusters and simultaneously binds ten cryptochromes. Through molecular dynamics we have analysed the stability of the ISCA1-cryptochrome complex and characterized the interaction at the binding sites between individual cryptochrome and ISCA1. It is found that the cryptochrome binding to the ISCA1 polymer is not uniform and that the binding affinity depends on its placement along the ISCA1 polymer. This finding supports the claim that the individual ISCA1 monomer acts as possible intracellular interaction partner of cryptochrome, but the proposed existence of an elongated ISCA1 polymer with multiple attached cryptochromes appears to be questionable.