RNF4 and TOPORS are SUMO-targeted ubiquitin ligases (STUbLs) required for arsenic trioxide–induced degradation of the PML-RARA oncoprotein, a critical therapeutic mechanism in the treatment of acute promyelocytic leukemia. Uniquely, TOPORS also functions as a SUMO E3 ligase, positioning it at the interface of SUMOylation and ubiquitination pathways. Mechanistic characterisation of these enzymes is challenging due to the transient nature of their interactions, which are frequently mediated by flexible and intrinsically disordered regions. Here, we employ activity-based photoreactive probes in combination with in-vitro crosslinking mass spectrometry to capture and map these dynamic complexes at residue-level resolution. This approach enables direct identification of interaction interfaces and provides new mechanistic insight into STUbL regulation and E3 ligase function.