Annotations: 6W8D

Structure of DNMT3A (R882H) in complex with CGT DNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth C]	G-alpha	e6w8dC1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: G-alpha	ECOD (v295.2)
B	G-alpha	e6w8dB1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: G-alpha	ECOD (v295.2)
C [auth D]	G-alpha	e6w8dD1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: G-alpha	ECOD (v295.2)
A	G-alpha	e6w8dA1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: G-alpha	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth C]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D]	PF00145	C-5 cytosine-specific DNA methylase (DNA_methylase)	C-5 cytosine-specific DNA methylase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F	CGT DNA (25-MER)	-	-	-
B, D [auth C]	DNA (cytosine-5)-methyltransferase 3-like	enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein binding binding enzyme binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation retrotransposition transposable element silencing by heterochromatin formation transposition transposable element silencing male meiosis I organelle fission meiotic cell cycle male meiotic nuclear division meiotic cell cycle process nuclear division organelle organization meiosis I meiosis I cell cycle process meiotic nuclear division cell cycle cell cycle process cellular developmental process cell development cellular process involved in reproduction in multicellular organism cell differentiation anatomical structure development epigenetic programming of gene expression genomic imprinting germ cell development stem cell differentiation regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation transposable element silencing by piRNA-mediated DNA methylation gene silencing by piRNA-directed DNA methylation piRNA-mediated heterochromatin formation negative regulation of DNA methylation-dependent heterochromatin formation negative regulation of heterochromatin formation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of chromatin organization negative regulation of cellular component organization regulation of cellular component organization positive regulation of biological process negative regulation of chromatin organization positive regulation of biosynthetic process positive regulation of cellular process positive regulation of gene expression regulation of heterochromatin organization negative regulation of heterochromatin organization	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle condensed chromosome nuclear lumen cytoplasm cytosol protein-containing complex histone methyltransferase complex catalytic complex nuclear protein-containing complex transferase complex PcG protein complex nucleoplasm methyltransferase complex ESC/E(Z) complex chromatin heterochromatin
A, C [auth D]	DNA (cytosine-5)-methyltransferase 3A	RNA binding binding lncRNA binding nucleic acid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding RNA binding binding lncRNA binding nucleic acid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding unmethylated CpG binding transcription corepressor activity transcription regulator activity transcription coregulator activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity transferase activity methyltransferase activity protein-cysteine methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid identical protein binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to stimulus response to chemical response to xenobiotic stimulus negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus regulation of cellular response to hypoxia positive regulation of biological process regulation of cellular response to stress positive regulation of response to stimulus regulation of response to stress positive regulation of cellular response to hypoxia positive regulation of cellular process regulation of response to stimulus response to nutrient levels response to lipid response to nutrient response to vitamin A response to vitamin developmental process multicellular organismal process cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development animal gross anatomical part developmental process system development response to toxic substance cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation response to ionizing radiation response to radiation response to metal ion response to lead ion hepatocyte apoptotic process apoptotic process cell death programmed cell death epithelial cell apoptotic process response to alcohol response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to alcohol cellular response to ethanol response to ethanol transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation retrotransposition transposable element silencing by heterochromatin formation transposition transposable element silencing by piRNA-mediated DNA methylation transposable element silencing gene silencing by piRNA-directed DNA methylation piRNA-mediated heterochromatin formation response to nitrogen compound response to cocaine response to alkaloid response to estradiol	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix XY body sex chromosome membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix XY body sex chromosome membraneless organelle intracellular membraneless organelle chromosome chromosome, centromeric region chromosomal region protein-containing complex catalytic complex cytoplasm nucleoplasm chromatin heterochromatin euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D [auth C]	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
B, D [auth C]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B, D [auth C]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B, D [auth C]	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
B, D [auth C]	IPR050390	DNA Cytosine-5 Methyltransferase	Family
B, D [auth C]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B, D [auth C]	IPR025766	ADD domain	Domain
A, C [auth D]	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
A, C [auth D]	IPR044108	DNA (cytosine-5)-methyltransferase 3A, ADD domain	Domain
A, C [auth D]	IPR000313	PWWP domain	Domain
A, C [auth D]	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A, C [auth D]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, C [auth D]	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
A, C [auth D]	IPR050390	DNA Cytosine-5 Methyltransferase	Family
A, C [auth D]	IPR001525	C-5 cytosine methyltransferase	Family
A, C [auth D]	IPR054724	DNA (cytosine-5)-methyltransferase, N-terminal	Domain
A, C [auth D]	IPR025766	ADD domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D [auth C]	: Q9UJW3	ankylosing spondylitis inflammatory bowel disease ulcerative colitis celiac disease rheumatoid arthritis Crohn disease schizophrenia
A, C [auth D]	: Q9Y6K1	tall stature-intellectual disability-facial dysmorphism syndrome Crohn disease acute monocytic leukemia juvenile myelomonocytic leukemia acute myeloid leukemia intellectual disability breast cancer chronic myelomonocytic leukemia primary cutaneous T-cell non-Hodgkin lymphoma acute promyelocytic leukemia breast carcinoma Clear-cell metastatic renal cell carcinoma mature T-cell and NK-cell non-Hodgkin lymphoma Sezary syndrome angioimmunoblastic T-cell lymphoma tall stature-intellectual disability-facial dysmorphism syndrome Crohn disease acute monocytic leukemia juvenile myelomonocytic leukemia acute myeloid leukemia intellectual disability breast cancer chronic myelomonocytic leukemia primary cutaneous T-cell non-Hodgkin lymphoma acute promyelocytic leukemia breast carcinoma Clear-cell metastatic renal cell carcinoma mature T-cell and NK-cell non-Hodgkin lymphoma Sezary syndrome angioimmunoblastic T-cell lymphoma microcephaly non-small cell lung carcinoma ductal breast carcinoma in situ pancreatic intraductal papillary-mucinous neoplasm genetic endocrine growth disease primary biliary cholangitis ileocolitis systemic mastocytosis atypical teratoid rhabdoid tumor lung cancer malignant ependymoma congenital anemia Crohn's colitis myelodysplastic syndrome oligodendroglioma glioblastoma hematologic disease large cell medulloblastoma autism spectrum disorder malignant glioma osteosarcoma plasma cell myeloma granulomatous slack skin disease primitive neuroectodermal tumor hypertensive disorder invasive ductal breast carcinoma lung benign neoplasm malignant mesothelioma cancer medulloblastoma

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.