5YX2

Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites

Functional Information from GO Data

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	binding site for residue GOL A 1001

Chain	Residue
A	HIS847
A	GLU856

---

site_id	AC2
Number of Residues	5
Details	binding site for residue GOL A 1002

Chain	Residue
A	PRO709
A	ASN711
A	ARG891
A	SAH1005
A	HOH1112

---

site_id	AC3
Number of Residues	4
Details	binding site for residue GOL A 1003

Chain	Residue
A	GOL1004
D	VAL809
A	ARG866
A	VAL872

---

site_id	AC4
Number of Residues	3
Details	binding site for residue GOL A 1004

Chain	Residue
A	HIS873
A	GOL1003
D	ARG676

---

site_id	AC5
Number of Residues	22
Details	binding site for residue SAH A 1005

Chain	Residue
A	PHE640
A	ASP641
A	GLY642
A	ILE643
A	THR645
A	SER663
A	GLU664
A	VAL665
A	CYS666
A	ASP686
A	VAL687
A	ARG688
A	GLY707
A	PRO709
A	LEU730
A	ARG891
A	SER892
A	TRP893
A	GOL1002
A	HOH1101
A	HOH1107
A	HOH1108

---

site_id	AC6
Number of Residues	4
Details	binding site for residue GOL D 1001

Chain	Residue
D	PHE751
D	PHE752
D	ASN797
F	DC423

---

site_id	AC7
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	HOH1104

---

site_id	AC8
Number of Residues	5
Details	binding site for residue GOL E 501

Chain	Residue
D	ASN711
D	THR835
D	ARG891
E	DG428
E	DT429

---

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

Chain	Residue
D	SER708
D	CYS710
D	SER714
D	ILE715
D	VAL716
D	GLU756
D	VAL758
D	ALA760
D	ARG790
D	ARG792
D	ARG831
D	THR832
D	THR834
D	GLY890
D	ARG891
E	DT425
E	DG428
F	DG442
F	DC443
F	DA444

---

site_id	AD1
Number of Residues	21
Details	binding site for Di-nucleotide PYO E 427 and DG E 428

Chain	Residue
E	DG426
E	DT429
E	GOL501
F	DC441
D	SER708
D	CYS710
D	ASN711
D	SER714
D	VAL716
D	ASN717
D	PRO718
D	GLU756
D	VAL758
D	ALA760
D	ARG790
D	ARG792
D	THR834
D	THR835
D	ARG836
D	GLY890
D	ARG891

---

site_id	AD2
Number of Residues	20
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	ALA760
A	ARG790
A	ARG792
A	ARG831
A	THR832
A	THR834
A	GLY890
A	ARG891
E	DG442
E	DC443
E	DA444
F	DT425
F	DG428

---

site_id	AD3
Number of Residues	24
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	ALA760
A	ARG790
A	ARG792
A	THR834
A	THR835
A	ARG836
A	GLY890
A	ARG891
A	HOH1102
E	DA440
E	DC441
F	DG426
F	DT429
F	HOH501
F	HOH506

---

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	556
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	2
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	18
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	2
Details	Modified residue: {"description":"S-methylcysteine; by autocatalysis","evidences":[{"source":"UniProtKB","id":"O88508","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---