In order to identify the structural determinants of cobrotoxin that caused its anomalous mobility in sodium dodecyl sulfate (SDS) gel, comparative studies on the capacities of cobrotoxin and its modified derivatives for binding with SDS were made. Cobrotoxin migrates faster in SDS gel after modification of Lys residues or carboxylated groups. However, the capacities of modified derivatives for binding with SDS molecules did not show a positive correlation with their electrophoretic mobilities. Moreover, it was found that the segment at positions 22-38 had the greatest capacity to bind with SDS than other segments of cobrotoxin, but guanidination of Lys residues of this peptide fragment did not significantly change its migration. These results suggest that the SDS-binding capacity of cobrotoxin is not solely responsible for its anomalous mobility in SDS gel, and that the effects may arise from the electrostatic interactions between Lys residue and carboxylated groups.