3SWC | pdb_00003swc

GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
A	SCOP2B Superfamily	SET domain	8004150	3000162	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CXC domain-like	8091567	3002037	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)
C [auth B]	FAA_hydrolase	e3swcB2	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: FAA_hydrolase	ECOD (develop294)
C [auth B]	LepA_C	e3swcB3	A: alpha bundles	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: LepA_C	ECOD (develop294)
A	FAA_hydrolase	e3swcA2	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: FAA_hydrolase	ECOD (develop294)
A	LepA_C	e3swcA3	A: alpha bundles	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: LepA_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
A	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 histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups histone H3K9 methyltransferase activity transferase activity histone H3K9 trimethyltransferase activity S-adenosylmethionine-dependent methyltransferase activity p53 binding protein binding binding transcription factor binding transcription coregulator binding transcription corepressor binding protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups histone H3K9 methyltransferase activity transferase activity histone H3K9 trimethyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity histone H3K9 monomethyltransferase activity histone H3K9me2 methyltransferase 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 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 fat cell differentiation cellular developmental process cell differentiation beige fat cell differentiation peptidyl-lysine methylation 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 epigenetic regulation of gene expression cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization negative regulation of gene expression constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic peptidyl-lysine monomethylation regulation of developmental process negative regulation of developmental process negative regulation of white fat cell differentiation white fat cell differentiation regulation of cell differentiation negative regulation of fat cell differentiation negative regulation of cell differentiation regulation of fat cell differentiation multicellular organismal process homeostatic process positive regulation of biological process adaptive thermogenesis 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 facultative heterochromatin formation response to stimulus response to chemical response to antibiotic response to fungicide response to toxic substance brown fat cell differentiation regulation of embryonic development regulation of multicellular organismal development 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 intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle 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 membraneless organelle intracellular membraneless organelle chromatin chromosome nuclear body
B [auth P], D [auth Q]	DNA (cytosine-5)-methyltransferase 3A	RNA binding binding lncRNA binding nucleic acid binding sequence-specific DNA binding DNA binding unmethylated CpG 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 RNA binding binding lncRNA binding nucleic acid binding sequence-specific DNA binding DNA binding unmethylated CpG 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 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 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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	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 response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels 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 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 cellular process methylation metabolic process response to nutrient levels 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 response to oxygen-containing compound cellular response to oxygen-containing 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 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 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 biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II 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 regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process 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 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 cellular component biogenesis cellular component assembly heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation response to metal ion response to lead ion cell development cellular process involved in reproduction in multicellular organism epigenetic programming of gene expression genomic imprinting autosome genomic imprinting germ cell development hepatocyte apoptotic process apoptotic process cell death programmed cell death epithelial cell apoptotic process regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation post-embryonic development 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	intracellular organelle XY body cellular anatomical structure intracellular anatomical structure sex chromosome organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm chromatin heterochromatin membrane-bounded organelle nucleus intracellular organelle XY body cellular anatomical structure intracellular anatomical structure sex chromosome organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm chromatin heterochromatin membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear lumen nuclear matrix chromosome, centromeric region chromosomal region protein-containing complex 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]	IPR054724	DNA (cytosine-5)-methyltransferase, N-terminal	Domain
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
B [auth P], D [auth Q]	IPR050390	DNA Cytosine-5 Methyltransferase	Family

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth P], D [auth Q]	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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.