Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6W89

Structure of DNMT3A (R882H) in complex with CGA DNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008168	molecular_function	methyltransferase activity
D	0008168	molecular_function	methyltransferase activity
G	0008168	molecular_function	methyltransferase activity
J	0008168	molecular_function	methyltransferase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue CIT A 1001

Chain	Residue
A	ARG803
A	ALA806
A	ARG899
A	HIS900
A	HOH1140

site_id	AC2
Number of Residues	16
Details	binding site for residue SAH A 1002

Chain	Residue
A	THR645
A	SER663
A	GLU664
A	VAL665
A	ASP686
A	VAL687
A	GLY707
A	ARG891
A	SER892
A	TRP893
A	HOH1123
A	HOH1146
A	PHE640
A	ASP641
A	GLY642
A	ILE643

site_id	AC3
Number of Residues	5
Details	binding site for residue CIT D 1001

Chain	Residue
D	ARG803
D	ALA806
D	THR808
D	ARG899
D	HIS900

site_id	AC4
Number of Residues	17
Details	binding site for residue SAH D 1002

Chain	Residue
D	PHE640
D	ASP641
D	GLY642
D	ILE643
D	THR645
D	SER663
D	GLU664
D	VAL665
D	CYS666
D	ASP686
D	VAL687
D	GLY707
D	LEU730
D	ARG891
D	SER892
D	TRP893
D	HOH1133

site_id	AC5
Number of Residues	5
Details	binding site for residue CIT G 1001

Chain	Residue
G	ARG803
G	ALA806
G	ARG899
G	HIS900
G	HOH1103

site_id	AC6
Number of Residues	20
Details	binding site for residue SAH G 1002

Chain	Residue
G	PHE640
G	ASP641
G	GLY642
G	ILE643
G	THR645
G	SER663
G	GLU664
G	VAL665
G	CYS666
G	ASP686
G	VAL687
G	GLY707
G	LEU730
G	ARG891
G	SER892
G	TRP893
G	HOH1112
G	HOH1117
G	HOH1121
G	HOH1156

site_id	AC7
Number of Residues	5
Details	binding site for residue CIT J 1001

Chain	Residue
J	ARG803
J	ALA806
J	THR808
J	ARG899
J	HIS900

site_id	AC8
Number of Residues	18
Details	binding site for residue SAH J 1002

Chain	Residue
J	PHE640
J	ASP641
J	GLY642
J	ILE643
J	THR645
J	SER663
J	GLU664
J	VAL665
J	CYS666
J	ASP686
J	VAL687
J	GLY707
J	LEU730
J	ARG891
J	SER892
J	TRP893
J	HOH1137
J	HOH1143

site_id	AC9
Number of Residues	20
Details	binding site for Di-nucleotide DG E 426 and PYO E 427

Chain	Residue
D	ARG792
D	ARG831
D	THR832
D	THR834
D	THR835
D	GLY890
D	ARG891
E	DT425
E	DG428
F	DG442
F	DC443
F	DA444
D	SER708
D	CYS710
D	SER714
D	ILE715
D	VAL716
D	GLU756
D	VAL758
D	ARG790

site_id	AD1
Number of Residues	19
Details	binding site for Di-nucleotide PYO E 427 and DG E 428

Chain	Residue
D	SER708
D	CYS710
D	ASN711
D	SER714
D	VAL716
D	ASN717
D	GLU756
D	VAL758
D	ARG790
D	ARG792
D	THR834
D	THR835
D	ASN838
D	GLY890
D	ARG891
E	DG426
E	DA429
F	DC441
F	DG442

site_id	AD2
Number of Residues	22
Details	binding site for Di-nucleotide DG F 426 and PYO F 427

Chain	Residue
A	SER708
A	CYS710
A	SER714
A	ILE715
A	VAL716
A	GLU756
A	VAL758
A	ARG790
A	ARG792
A	ARG831
A	THR832
A	THR834
A	THR835
A	GLY890
A	ARG891
E	DG442
E	DC443
E	DA444
F	DT425
F	DG428
F	HOH501
F	HOH502

site_id	AD3
Number of Residues	22
Details	binding site for Di-nucleotide PYO F 427 and DG F 428

Chain	Residue
A	SER708
A	CYS710
A	ASN711
A	SER714
A	VAL716
A	ASN717
A	PRO718
A	GLU756
A	VAL758
A	ARG790
A	ARG792
A	THR834
A	THR835
A	ASN838
A	GLY890
A	ARG891
A	HOH1109
E	DC441
E	DG442
F	DG426
F	DA429
F	HOH502

site_id	AD4
Number of Residues	23
Details	binding site for Di-nucleotide DG K 426 and PYO K 427

Chain	Residue
J	SER708
J	CYS710
J	SER714
J	ILE715
J	VAL716
J	GLU756
J	VAL758
J	ARG790
J	ARG792
J	ARG831
J	THR832
J	THR834
J	THR835
J	GLY890
J	ARG891
J	HOH1143
K	DT425
K	DG428
K	HOH503
K	HOH504
L	DG442
L	DC443
L	DA444

site_id	AD5
Number of Residues	19
Details	binding site for Di-peptide PYO K 427 and CYS J 710

Chain	Residue
J	SER708
J	PRO709
J	ASN711
J	ASP712
J	LEU713
J	SER714
J	GLU756
J	ASN757
J	VAL758
J	ARG790
J	ARG792
J	THR834
J	THR835
J	GLY890
J	ARG891
J	HOH1143
K	DG426
K	DG428
K	HOH503

site_id	AD6
Number of Residues	24
Details	binding site for Di-nucleotide PYO K 427 and DG K 428

Chain	Residue
J	SER708
J	CYS710
J	ASN711
J	SER714
J	VAL716
J	ASN717
J	PRO718
J	GLU756
J	VAL758
J	ARG790
J	ARG792
J	THR834
J	THR835
J	ASN838
J	GLY890
J	ARG891
J	HOH1109
J	HOH1143
K	DG426
K	DA429
K	HOH502
K	HOH503
L	DC441
L	DG442

site_id	AD7
Number of Residues	24
Details	binding site for Di-nucleotide DG L 426 and PYO L 427

Chain	Residue
G	SER708
G	CYS710
G	SER714
G	ILE715
G	VAL716
G	GLU756
G	VAL758
G	ARG790
G	ARG792
G	ARG831
G	THR832
G	THR834
G	THR835
G	GLY890
G	ARG891
G	HOH1156
K	DG442
K	DC443
K	DA444
L	DT425
L	DG428
L	HOH501
L	HOH503
L	HOH504

site_id	AD8
Number of Residues	25
Details	binding site for Di-nucleotide PYO L 427 and DG L 428

Chain	Residue
G	SER708
G	CYS710
G	ASN711
G	SER714
G	VAL716
G	ASN717
G	PRO718
G	GLU756
G	VAL758
G	ARG790
G	ARG792
G	THR834
G	THR835
G	ARG836
G	ASN838
G	GLY890
G	ARG891
G	HOH1111
G	HOH1156
K	DC441
K	DG442
L	DG426
L	DA429
L	HOH501
L	HOH504

site_id	AD9
Number of Residues	19
Details	binding site for Di-peptide PYO L 427 and CYS G 710

Chain	Residue
G	SER708
G	PRO709
G	ASN711
G	ASP712
G	LEU713
G	SER714
G	GLU756
G	ASN757
G	VAL758
G	ARG790
G	ARG792
G	THR834
G	THR835
G	GLY890
G	ARG891
G	HOH1156
L	DG426
L	DG428
L	HOH504

Functional Information from PROSITE/UniProt

site_id	PS00094
Number of Residues	13
Details	C5_MTASE_1 C-5 cytosine-specific DNA methylases active site. DlVigGsPCnDLS

Chain	Residue	Details
A	ASP702-SER714

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1112
Details	Domain: {"description":"SAM-dependent MTase C5-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU01016","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01016","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10018","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"17713477","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2QRV","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"S-methylcysteine; by autocatalysis","evidences":[{"source":"UniProtKB","id":"O88508","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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