6KDB | pdb_00006kdb

Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpT site

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)
C	DNA_methylase_1	e6kdbC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase_1	ECOD (1.6)
B	DNA_methylase_1	e6kdbB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase_1	ECOD (1.6)
D	DNA_methylase_1	e6kdbD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase_1	ECOD (1.6)
A	DNA_methylase_1	e6kdbA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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, 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	DNA (25-MER)	-	-	-
B, C	DNA (cytosine-5)-methyltransferase 3-like	enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding protein 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 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 placenta development animal organ development anatomical structure development methylation extraembryonic membrane development chorion development cellular developmental process cell differentiation chorionic trophoblast cell differentiation epigenetic programming of gene expression epigenetic programming in the zygotic pronuclei epigenetic programing of female pronucleus heterochromatin formation constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation retrotransposition transposable element silencing by heterochromatin formation transposition transposable element silencing cell development cellular process involved in reproduction in multicellular organism genomic imprinting autosome genomic imprinting germ cell development 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 stem cell differentiation multicellular organism development multicellular organismal process post-embryonic development 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 regulation of cellular component organization negative regulation of DNA methylation-dependent heterochromatin formation negative regulation of heterochromatin formation positive regulation of biological process negative regulation of chromatin organization positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of heterochromatin formation regulation of chromatin organization negative regulation of cellular component organization positive regulation of gene expression	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, D	DNA (cytosine-5)-methyltransferase 3B	DNA binding 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 DNA binding 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 transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process methylation 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 transcription by RNA polymerase II 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 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 nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	protein-containing complex catalytic complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, C	Pharos: Q9UJW3	ankylosing spondylitis inflammatory bowel disease ulcerative colitis celiac disease rheumatoid arthritis Crohn disease schizophrenia
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

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.