Annotations: 6KDP

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00145	e6kdpA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF00145	ECOD (1.6)
D	PF00145	e6kdpD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF00145	ECOD (1.6)
B	F_UNCLASSIFIED	e6kdpB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e6kdpC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
C	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, 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
A, D	DNA (cytosine-5)-methyltransferase 3B	DNA binding binding organic cyclic compound binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity cation binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process cellular metabolic process regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process	protein-containing complex catalytic complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B, C	DNA (cytosine-5)-methyltransferase 3-like	DNA binding binding organic cyclic compound binding nucleic acid binding DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity DNA binding binding organic cyclic compound binding nucleic acid binding DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein binding enzyme binding cation binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation placenta development animal organ development anatomical structure development extraembryonic membrane development chorion development cellular developmental process cell differentiation chorionic trophoblast cell differentiation protein-DNA complex organization cellular component organization chromatin organization DNA methylation-dependent heterochromatin formation chromatin remodeling cellular component organization or biogenesis heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of gene expression facultative heterochromatin formation negative regulation of gene expression, epigenetic epigenetic programming in the zygotic pronuclei epigenetic programing of female pronucleus epigenetic programming of gene expression cell development cellular process involved in reproduction in multicellular organism genomic imprinting autosome genomic imprinting germ cell development retrotransposon silencing by heterochromatin formation retrotransposon silencing transposition retrotransposition 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 transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II stem cell differentiation 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 DNA methylation-dependent heterochromatin formation regulation of cellular component organization positive regulation of biological process positive regulation of cellular metabolic process negative regulation of chromatin organization positive regulation of biosynthetic process positive regulation of cellular process positive regulation of gene expression positive regulation of cellular biosynthetic process	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle condensed chromosome non-membrane-bounded organelle 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 protein-DNA complex chromatin heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
A, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, D	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
A, D	IPR000313	PWWP domain	Domain
A, D	IPR030488	DNA (cytosine-5)-methyltransferase 3B, ADD domain	Domain
A, D	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A, D	IPR001525	C-5 cytosine methyltransferase	Family
A, D	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, D	IPR025766	ADD domain	Domain
B, C	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
B, C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B, C	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B, C	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
B, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B, C	IPR025766	ADD domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D	Pharos: Q9UBC3	immunodeficiency-centromeric instability-facial anomalies syndrome 1 primary immunodeficiency disease breast carcinoma facioscapulohumeral muscular dystrophy 2 Craniofacial Abnormalities prostate cancer carcinoma sarcomatoid carcinoma immunodeficiency-centromeric instability-facial anomalies syndrome intellectual disability lung adenocarcinoma medulloblastoma non-small cell lung carcinoma autism spectrum disorder schizophrenia immunodeficiency-centromeric instability-facial anomalies syndrome 1 primary immunodeficiency disease breast carcinoma facioscapulohumeral muscular dystrophy 2 Craniofacial Abnormalities prostate cancer carcinoma sarcomatoid carcinoma immunodeficiency-centromeric instability-facial anomalies syndrome intellectual disability lung adenocarcinoma medulloblastoma non-small cell lung carcinoma autism spectrum disorder schizophrenia hereditary diffuse gastric adenocarcinoma invasive ductal breast carcinoma malignant mesothelioma ovarian cancer primitive neuroectodermal tumor cancer undifferentiated carcinoma gastric cancer inflammatory bowel disease large cell medulloblastoma nicotine dependence atypical teratoid rhabdoid tumor polycystic ovary syndrome breast cancer gastric neoplasm
B, C	Pharos: Q9UJW3	ankylosing spondylitis inflammatory bowel disease ulcerative colitis celiac disease rheumatoid arthritis Crohn disease schizophrenia

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.