Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3SWR

Structure of human DNMT1 (601-1600) in complex with Sinefungin

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 PDB Data

site_id	AC1
Number of Residues	20
Details	BINDING SITE FOR RESIDUE SFG A 300

Chain	Residue
A	HOH58
A	GLU1168
A	MET1169
A	TRP1170
A	ASP1190
A	CYS1191
A	PRO1225
A	LEU1247
A	GLU1266
A	ASN1578
A	ALA1579
A	EDO119
A	VAL1580
A	HOH258
A	PHE1145
A	SER1146
A	GLY1147
A	GLY1149
A	GLY1150
A	LEU1151

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 1

Chain	Residue
A	LEU623
A	GLU846
A	ARG1259
A	ARG1289

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MES A 2

Chain	Residue
A	HOH46
A	PRO1182
A	GLY1183
A	THR1185
A	GLN1209

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MES A 4

Chain	Residue
A	ARG778
A	HIS795
A	LEU816
A	TYR836
A	TYR865
A	VAL894

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 101

Chain	Residue
A	EDO117
A	GLY1305
A	TRP1395
A	PHE1396

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 102

Chain	Residue
A	HOH6
A	PHE1296
A	GLY1297
A	VAL1298
A	LEU1341
A	PHE1350
A	VAL1351
A	SER1352

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 103

Chain	Residue
A	GLY1058
A	ARG1059
A	ASN1081
A	ARG1356

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 104

Chain	Residue
A	EDO107
A	LEU1326
A	GLU1591
A	LEU1594

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 105

Chain	Residue
A	EDO107
A	HOH255
A	LYS1593

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 106

Chain	Residue
A	TYR1035
A	HIS1036
A	ARG1368
A	ASP1369
A	SER1372
A	GLN1393
A	SER1394

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 107

Chain	Residue
A	HOH25
A	EDO104
A	EDO105
A	PRO1080

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 108

Chain	Residue
A	ASP870
A	ARG875
A	LEU1326

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 109

Chain	Residue
A	TRP868
A	GLU877
A	SER878
A	PRO880
A	ARG898

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 110

Chain	Residue
A	ASP706
A	ARG1269
A	SER1273
A	VAL1343
A	VAL1344

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 111

Chain	Residue
A	VAL964
A	TYR969
A	HIS972
A	PRO1429
A	ASP1438

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 112

Chain	Residue
A	HOH262
A	PRO988
A	VAL1333
A	PHE1334
A	CYS1339
A	LEU1357
A	SER1358

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 113

Chain	Residue
A	ARG1276
A	SER1277
A	VAL1345
A	ASP1346

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 114

Chain	Residue
A	LEU774
A	TYR775
A	LEU776
A	PHE797
A	ALA799
A	ASP802
A	HIS719

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 115

Chain	Residue
A	LYS716
A	GLN720
A	GLU1202
A	THR1204

site_id	CC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 116

Chain	Residue
A	TRP1165
A	ARG1210

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 117

Chain	Residue
A	HOH24
A	EDO101
A	EDO118
A	HOH278
A	ILE1039
A	HIS1332
A	TRP1395

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 118

Chain	Residue
A	EDO117
A	HOH277
A	ASN1040
A	SER1076
A	ARG1082
A	TRP1395

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 119

Chain	Residue
A	SFG300
A	GLY1223
A	GLU1266
A	ASN1267
A	ARG1312
A	ASN1578

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 120

Chain	Residue
A	VAL705
A	ARG1311
A	ARG1337
A	ALA1338

site_id	CC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 121

Chain	Residue
A	CYS653
A	ASN1529

site_id	CC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 122

Chain	Residue
A	GLY654
A	TRP1510
A	MET1533

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 123

Chain	Residue
A	PRO1429
A	LEU1430
A	ALA1431

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 124

Chain	Residue
A	EDO125
A	THR1366
A	ASP1520

site_id	DC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 125

Chain	Residue
A	HOH53
A	HOH83
A	EDO124
A	THR1031

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1601

Chain	Residue
A	CYS653
A	CYS656
A	CYS659
A	CYS691

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 1602

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

site_id	DC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 3

Chain	Residue
A	HIS793
A	CYS820
A	CYS893
A	CYS896

site_id	DC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1603

Chain	Residue
A	CYS1476
A	CYS1478
A	CYS1485
A	HIS1502

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	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_FI4
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_FI5
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_FI6
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_FI7
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18220336

Chain	Residue	Details
A	SER732

site_id	SWS_FT_FI8
Number of Residues	8
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:21947282

Chain	Residue	Details
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:23186163

Chain	Residue	Details
A	SER878

site_id	SWS_FT_FI10
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_FI11
Number of Residues	1
Details	MOD_RES: N6-acetyllysine; by EHMT2 => ECO:0000269\|PubMed:21947282

Chain	Residue	Details
A	LYS1117

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P13864

Chain	Residue	Details
A	LYS1119
A	LYS1121

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