3SW9

GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	CXC domain-like	8091567	3002037	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SET domain	8004150	3000162	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	CXC domain-like	8091567	3002037	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	SET domain	8004150	3000162	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SET	e3sw9A2	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET	ECOD (1.6)
A	Pre-SET	e3sw9A1	A: few secondary structure elements	X: Zn3Cys9 preSET domain-related (From Topology)	H: Zn3Cys9 preSET domain-related (From Topology)	T: Zn3Cys9 preSET domain-related	F: Pre-SET	ECOD (1.6)
C [auth B]	SET	e3sw9B2	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET	ECOD (1.6)
C [auth B]	Pre-SET	e3sw9B1	A: few secondary structure elements	X: Zn3Cys9 preSET domain-related (From Topology)	H: Zn3Cys9 preSET domain-related (From Topology)	T: Zn3Cys9 preSET domain-related	F: Pre-SET	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
C [auth B]	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF00856	SET domain (SET)	SET domain	-	Family
A, C [auth B]	PF05033	Pre-SET motif (Pre-SET)	Pre-SET motif	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Histone-lysine N-methyltransferase EHMT1	p53 binding protein binding binding transcription factor binding transcription coregulator binding transcription corepressor binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity p53 binding protein binding binding transcription factor binding transcription coregulator binding transcription corepressor binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity histone H3 methyltransferase activity histone H3K9me2 methyltransferase activity histone H3K9 methyltransferase activity histone methyltransferase activity histone modifying activity C2H2 zinc finger domain binding protein domain specific binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H3K27 methyltransferase activity	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 peptidyl-lysine methylation organonitrogen compound metabolic process protein methylation peptidyl-lysine modification macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process peptidyl-lysine dimethylation peptidyl-lysine monomethylation multicellular organismal process homeostatic process positive regulation of biological process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process regulation of multicellular organismal process protein-DNA complex organization cellular component organization chromatin organization 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 response to stimulus response to chemical response to antibiotic response to fungicide response to toxic substance developmental process regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development multicellular organism development anatomical structure development transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	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 protein-containing complex protein-DNA 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 protein-containing complex protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle nuclear body
B [auth P], D [auth Q]	DNA (cytosine-5)-methyltransferase 3A	sequence-specific DNA binding DNA binding binding organic cyclic compound binding unmethylated CpG binding nucleic acid binding 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 sequence-specific DNA binding DNA binding binding organic cyclic compound binding unmethylated CpG binding nucleic acid binding 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 cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor 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 protein-containing complex binding chromatin binding DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates	response to stimulus response to chemical response to xenobiotic stimulus developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of cellular process cellular biosynthetic process negative regulation of biological process response to stimulus response to chemical response to xenobiotic stimulus developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process 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 response to nutrient levels response to organic substance response to lipid response to nutrient response to vitamin A response to vitamin response to toxic substance response to ionizing radiation response to radiation cellular response to bisphenol A cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to organic substance response to organic cyclic compound response to bisphenol A cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid response to alcohol cellular response to alcohol cellular response to ethanol response to ethanol 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 primary metabolic process organic cyclic compound metabolic 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 regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process 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 multicellular organismal process cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development system development DNA methylation-dependent heterochromatin formation heterochromatin formation facultative heterochromatin formation epigenetic programming of gene expression response to metal ion response to lead ion response to inorganic substance cell development cellular process involved in reproduction in multicellular organism genomic imprinting autosome genomic imprinting germ cell development hepatocyte apoptotic process apoptotic process cell death programmed cell death epithelial cell apoptotic process response to organonitrogen compound response to nitrogen compound response to cocaine response to alkaloid response to estradiol	intracellular organelle XY body intracellular anatomical structure sex chromosome organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle cytoplasm protein-containing complex protein-DNA complex chromatin heterochromatin intracellular organelle XY body intracellular anatomical structure sex chromosome organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle cytoplasm protein-containing complex protein-DNA complex chromatin heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen nuclear matrix chromosome, centromeric region chromosomal region catalytic complex nucleoplasm euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR043550	Histone-lysine N-methyltransferase EHMT1/EHMT2	Family
A, C [auth B]	IPR007728	Pre-SET domain	Domain
A, C [auth B]	IPR046341	SET domain superfamily	Homologous Superfamily
A, C [auth B]	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, C [auth B]	IPR001214	SET domain	Domain
A, C [auth B]	IPR047762	EHMT1/2, cysteine-rich region	Domain
A, C [auth B]	IPR002110	Ankyrin repeat	Repeat
A, C [auth B]	IPR038035	Histone-lysine N-methyltransferase EHMT1, SET domain	Domain
B [auth P], D [auth Q]	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
B [auth P], D [auth Q]	IPR044108	DNA (cytosine-5)-methyltransferase 3A, ADD domain	Domain
B [auth P], D [auth Q]	IPR000313	PWWP domain	Domain
B [auth P], D [auth Q]	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
B [auth P], D [auth Q]	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
B [auth P], D [auth Q]	IPR001525	C-5 cytosine methyltransferase	Family
B [auth P], D [auth Q]	IPR025766	ADD domain	Domain
B [auth P], D [auth Q]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth B]	Pharos: Q9H9B1	medulloblastoma Kleefstra syndrome Kleefstra syndrome 1 adult medulloblastoma medullomyoblastoma with myogenic differentiation childhood medulloblastoma intellectual disability melanotic medulloblastoma rheumatoid arthritis desmoplastic/nodular medulloblastoma juvenile dermatomyositis large cell medulloblastoma oligodendroglioma pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor medulloblastoma Kleefstra syndrome Kleefstra syndrome 1 adult medulloblastoma medullomyoblastoma with myogenic differentiation childhood medulloblastoma intellectual disability melanotic medulloblastoma rheumatoid arthritis desmoplastic/nodular medulloblastoma juvenile dermatomyositis large cell medulloblastoma oligodendroglioma pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor Epileptic encephalopathy malignant ependymoma osteosarcoma primitive neuroectodermal tumor ovarian cancer

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.