7XI9
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)
This is a non-PDB format compatible entry.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003682 | molecular_function | chromatin binding |
| A | 0003886 | molecular_function | DNA (cytosine-5-)-methyltransferase activity |
| A | 0005634 | cellular_component | nucleus |
| A | 0006346 | biological_process | DNA methylation-dependent heterochromatin formation |
| A | 0008168 | molecular_function | methyltransferase activity |
| A | 0008270 | molecular_function | zinc ion binding |
Functional Information from PROSITE/UniProt
| site_id | PS00094 |
| Number of Residues | 13 |
| Details | C5_MTASE_1 C-5 cytosine-specific DNA methylases active site. EmLcgGpPCqGFS |
| Chain | Residue | Details |
| A | GLU1218-SER1230 |
| site_id | PS00095 |
| Number of Residues | 19 |
| Details | C5_MTASE_2 C-5 cytosine-specific DNA methylases C-terminal signature. RqvGNAVpPpLakaIgleI |
| Chain | Residue | Details |
| A | ARG1574-ILE1592 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 46 |
| Details | ZN_FING: CXXC-type => ECO:0000255|PROSITE-ProRule:PRU00509 |
| Chain | Residue | Details |
| A | ASN646-PRO692 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | ACT_SITE: |
| Chain | Residue | Details |
| A | CYS1226 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | CYS353 | |
| A | CYS356 | |
| A | CYS414 | |
| A | HIS418 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00509 |
| Chain | Residue | Details |
| A | CYS653 | |
| A | CYS656 | |
| A | CYS659 | |
| A | CYS664 | |
| A | CYS667 | |
| A | CYS670 | |
| A | CYS686 | |
| A | CYS691 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P13864 |
| Chain | Residue | Details |
| A | SER1146 | |
| A | GLY1150 | |
| A | ASP1190 | |
| A | VAL1580 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 3 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:21163962, ECO:0007744|PDB:3PTA |
| Chain | Residue | Details |
| A | GLU1168 | |
| A | CYS1191 | |
| A | ASN1578 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | SITE: Important for activity => ECO:0000250 |
| Chain | Residue | Details |
| A | SER509 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 9 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:21947282 |
| Chain | Residue | Details |
| A | LYS366 | |
| A | LYS749 | |
| A | LYS891 | |
| A | LYS957 | |
| A | LYS961 | |
| A | LYS975 | |
| A | LYS1054 | |
| A | LYS1349 | |
| A | LYS1415 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER394 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 3 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER398 | |
| A | SER549 | |
| A | SER878 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P13864 |
| Chain | Residue | Details |
| A | SER509 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER714 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18220336 |
| Chain | Residue | Details |
| A | SER732 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 3 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:21947282, ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS1111 | |
| A | LYS1113 | |
| A | LYS1115 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-acetyllysine; by EHMT2 => ECO:0000269|PubMed:21947282 |
| Chain | Residue | Details |
| A | LYS1117 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P13864 |
| Chain | Residue | Details |
| A | LYS1119 | |
| A | LYS1121 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS1609 |
