Structural analyses of a hereditary abnormal antithrombin III, antithrombin III Toyama, which has normal progressive antithrombin activity but no heparin cofactor activity, have been carried out to elucidate the molecular abnormality causing recurrent thrombophlebitis of a patient and to identify an amino acid residue essential for the binding with heparin. Abnormal antithrombin III was reduced, S-pyridylethylated, and treated with cyanogen bromide. Eleven fragments were isolated by the combination of Sephadex G-50 gel filtration and reversed-phase HPLC and compared with those from normal antithrombin III. One large fragment (CN-III) that appeared to have a different amino acid composition from that of the corresponding fragment from normal antithrombin III was digested with trypsin, and the digests were separated by HPLC. The abnormal peptide was identified by comparing the peptide map with that from normal antithrombin III. Amino acid sequence analysis of the abnormal peptide indicated that the arginine-47 of normal antithrombin III had been replaced by cysteine in antithrombin III Toyama. One base mutation, C leads to T, in the 5' terminal position of the arginine-47 genetic codon (CGT) is probably responsible for this substitution. These results also suggest that arginine-47 is an essential amino acid residue for the binding with heparin.