| Domain | Name | Category | Type |
| IPR001497 | Methylated-DNA-[protein]-cysteine S-methyltransferase, active site | Site | Active site |
| IPR008332 | Methylguanine DNA methyltransferase, ribonuclease-like domain | Domain | Domain |
| IPR014048 | Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding | Domain | Domain |
| IPR036217 | Methylated DNA-protein cysteine methyltransferase, DNA binding domain | Family | Homologous superfamily |
| IPR036388 | Winged helix-like DNA-binding domain superfamily | Family | Homologous superfamily |
| IPR036631 | Methylated DNA-protein cysteine methyltransferase domain superfamily | Family | Homologous superfamily |