3A1B

Crystal structure of the DNMT3A ADD domain in complex with histone H3

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0010468	biological_process	regulation of gene expression
A	0030527	molecular_function	structural constituent of chromatin

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1

Chain	Residue
A	CYS494
A	CYS497
A	CYS514
A	CYS517

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 2

Chain	Residue
A	CYS537
A	CYS540
A	CYS559
A	CYS562

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 3

Chain	Residue
A	CYS554
A	CYS583
A	CYS586
A	CYS549

---

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 615

Chain	Residue
A	EDO7
A	HOH9
A	PHE521
A	CYS524
A	GLN534
A	TYR536
A	CYS537
A	ARG556

---

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 616

Chain	Residue
A	GLU491
A	LEU504
A	GLU505
A	GLY511
A	GLY512
A	ARG598

---

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 617

Chain	Residue
A	GLU477
A	ALA525
A	TYR526
A	TYR528
A	ASP564
A	PRO569

---

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 4

Chain	Residue
A	TRP581
A	ASN582
A	TYR592

---

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 5

Chain	Residue
A	HOH21
A	ARG478
A	TYR481
A	GLU523
A	TYR526
A	GLN527

---

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 6

Chain	Residue
A	GLY543
A	ARG544
A	GLU545
A	CYS559
A	VAL560
A	GLU561

---

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

Chain	Residue
A	PHE521
A	ALA525
A	GLN534
A	ARG556
A	PRO569
A	LEU605
A	EDO615

---

Functional Information from PROSITE/UniProt

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
A	LYS469-LEU475

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Modified residue: {"description":"Citrulline; alternate","evidences":[{"source":"PubMed","id":"16567635","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by HASPIN and VRK1","evidences":[{"source":"PubMed","id":"15681610","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31527692","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16457588","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	Modified residue: {"description":"5-glutamyl serotonin; alternate","evidences":[{"source":"PubMed","id":"30867594","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine; by PKC","evidences":[{"source":"PubMed","id":"20228790","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Modified residue: {"description":"Symmetric dimethylarginine; by PRMT5; alternate","evidences":[{"source":"UniProtKB","id":"P68433","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"11242053","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16457588","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	Modified residue: {"description":"Citrulline; alternate","evidences":[{"source":"PubMed","id":"15345777","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16497732","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16567635","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Lipidation: {"description":"N6-decanoyllysine","evidences":[{"source":"PubMed","id":"35939806","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	30
Details	Zinc finger: {"description":"GATA-type; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU00865","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	56
Details	Zinc finger: {"description":"PHD-type; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU00865","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	92
Details	Region: {"description":"Interaction with the PRC2/EED-EZH2 complex","evidences":[{"source":"UniProtKB","id":"O88508","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---