Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4WXX

The crystal structure of human DNMT1(351-1600)

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
B	0003677	molecular_function	DNA binding
B	0003682	molecular_function	chromatin binding
B	0003886	molecular_function	DNA (cytosine-5-)-methyltransferase activity
B	0005634	cellular_component	nucleus
B	0006346	biological_process	DNA methylation-dependent heterochromatin formation
B	0008168	molecular_function	methyltransferase activity
B	0008270	molecular_function	zinc ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN A 1701

Chain	Residue
A	CYS1476
A	CYS1478
A	CYS1485
A	HIS1502

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN A 1702

Chain	Residue
A	HIS793
A	CYS820
A	CYS893
A	CYS896

site_id	AC3
Number of Residues	5
Details	binding site for residue ZN A 1703

Chain	Residue
A	GLY665
A	CYS667
A	CYS670
A	CYS686
A	CYS664

site_id	AC4
Number of Residues	5
Details	binding site for residue ZN A 1704

Chain	Residue
A	CYS653
A	GLY654
A	CYS656
A	CYS659
A	CYS691

site_id	AC5
Number of Residues	4
Details	binding site for residue ZN A 1705

Chain	Residue
A	CYS353
A	CYS356
A	CYS414
A	HIS418

site_id	AC6
Number of Residues	19
Details	binding site for residue SAH A 1706

Chain	Residue
A	PHE1145
A	SER1146
A	GLY1147
A	CYS1148
A	GLY1150
A	LEU1151
A	GLU1168
A	MET1169
A	TRP1170
A	GLU1189
A	ASP1190
A	CYS1191
A	GLY1223
A	LEU1247
A	ASN1578
A	ALA1579
A	VAL1580
A	HOH1918
A	HOH2051

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN B 1701

Chain	Residue
B	CYS1476
B	CYS1478
B	CYS1485
B	HIS1502

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN B 1702

Chain	Residue
B	HIS793
B	CYS820
B	CYS893
B	CYS896

site_id	AC9
Number of Residues	6
Details	binding site for residue ZN B 1703

Chain	Residue
B	CYS664
B	GLY665
B	CYS667
B	CYS670
B	CYS686
B	GLN687

site_id	AD1
Number of Residues	5
Details	binding site for residue ZN B 1704

Chain	Residue
B	CYS653
B	GLY654
B	CYS656
B	CYS659
B	CYS691

site_id	AD2
Number of Residues	4
Details	binding site for residue ZN B 1705

Chain	Residue
B	CYS353
B	CYS356
B	CYS414
B	HIS418

site_id	AD3
Number of Residues	17
Details	binding site for residue SAH B 1706

Chain	Residue
B	PHE1145
B	SER1146
B	GLY1147
B	GLY1150
B	LEU1151
B	GLU1168
B	MET1169
B	TRP1170
B	GLU1189
B	ASP1190
B	CYS1191
B	GLY1223
B	LEU1247
B	ASN1578
B	ALA1579
B	VAL1580
B	HOH1974

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	92
Details	ZN_FING: CXXC-type => ECO:0000255\|PROSITE-ProRule:PRU00509

Chain	Residue	Details
A	GLY982-HIS1028
B	GLY982-HIS1028

site_id	SWS_FT_FI2
Number of Residues	2
Details	ACT_SITE:

Chain	Residue	Details
A	THR1562
B	THR1562

site_id	SWS_FT_FI3
Number of Residues	8
Details	BINDING:

Chain	Residue	Details
A	ARG689
A	PRO692
A	VAL750
A	ALA754
B	ARG689
B	PRO692
B	VAL750
B	ALA754

site_id	SWS_FT_FI4
Number of Residues	16
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00509

Chain	Residue	Details
A	GLU989
B	ARG992
B	ARG995
B	PHE1000
B	LYS1003
B	ASN1006
B	TYR1022
B	THR1027
A	ARG992
A	ARG995
A	PHE1000
A	LYS1003
A	ASN1006
A	TYR1022
A	THR1027
B	GLU989

site_id	SWS_FT_FI5
Number of Residues	6
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P13864

Chain	Residue	Details
A	GLY1482
A	ASP1486
A	THR1526
B	GLY1482
B	ASP1486
B	THR1526

site_id	SWS_FT_FI6
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:21163962, ECO:0007744\|PDB:3PTA

Chain	Residue	Details
A	GLY1504
A	VAL1527
B	GLY1504
B	VAL1527

site_id	SWS_FT_FI7
Number of Residues	2
Details	SITE: Important for activity => ECO:0000250

Chain	Residue	Details
A	MET845
B	MET845

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000269\|PubMed:18438403

Chain	Residue	Details
A	LYS406
B	LYS406

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17081983, ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:19690332, ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	GLU463
B	GLU463

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:21406692

Chain	Residue	Details
A	PHE469
B	PHE469

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	GLU473
A	MET502
B	GLU473
B	MET502

site_id	SWS_FT_FI12
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P13864

Chain	Residue	Details
A	ILE477
A	MET845
B	ILE477
B	MET845

site_id	SWS_FT_FI13
Number of Residues	2
Details	MOD_RES: N6-methyllysine; by SETD7 => ECO:0000269\|PubMed:21151116

Chain	Residue	Details
A	GLY478
B	GLY478

site_id	SWS_FT_FI14
Number of Residues	2
Details	MOD_RES: Phosphoserine; by PKB/AKT1 => ECO:0000269\|PubMed:21151116, ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	PHE479
B	PHE479

site_id	SWS_FT_FI15
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18669648

Chain	Residue	Details
A	LEU488
B	LEU488

site_id	SWS_FT_FI16
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000269\|PubMed:21565170, ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	ASP490
B	ASP490

site_id	SWS_FT_FI17
Number of Residues	18
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:21947282

Chain	Residue	Details
A	ALA496
B	ALA496
B	TYR524
B	ASP702
B	PHE1085
B	GLN1227
B	GLN1293
B	GLY1297
B	ARG1311
B	GLY1390
A	TYR524
A	ASP702
A	PHE1085
A	GLN1227
A	GLN1293
A	GLY1297
A	ARG1311
A	GLY1390

site_id	SWS_FT_FI18
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	SER509
B	SER509

site_id	SWS_FT_FI19
Number of Residues	2
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0000269\|PubMed:21947282

Chain	Residue	Details
A	ARG595
B	ARG595

site_id	SWS_FT_FI20
Number of Residues	8
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	PHE648
A	VAL734
A	THR885
A	LYS1214
B	PHE648
B	VAL734
B	THR885
B	LYS1214

site_id	SWS_FT_FI21
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	ARG730
B	ARG730

site_id	SWS_FT_FI22
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17081983, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	VAL1050
B	VAL1050

site_id	SWS_FT_FI23
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18220336

Chain	Residue	Details
A	LEU1068
B	LEU1068

site_id	SWS_FT_FI24
Number of Residues	6
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:21947282, ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	SER1447
A	GLY1449
A	MET1451
B	SER1447
B	GLY1449
B	MET1451

site_id	SWS_FT_FI25
Number of Residues	2
Details	MOD_RES: N6-acetyllysine; by EHMT2 => ECO:0000269\|PubMed:21947282

Chain	Residue	Details
A	ARG1453
B	ARG1453

site_id	SWS_FT_FI26
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P13864

Chain	Residue	Details
A	LEU1455
A	TYR1457
B	LEU1455
B	TYR1457

site_id	SWS_FT_FI27
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
A	ARG595
B	ARG595

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)