9YKS | pdb_00009yks

Crystal structure of the G9a (EHMT2) SET domain in complex with SAM and TNG917

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D	SCOP2B Superfamily	SET domain	8088641	3000162	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CXC domain-like	8092240	3002037	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SET domain	8088641	3000162	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CXC domain-like	8092240	3002037	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CXC domain-like	8092240	3002037	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SET domain	8088641	3000162	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SET domain	8088641	3000162	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CXC domain-like	8092240	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)
D	ClpB_D2-small	e9yksD1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: ClpB_D2-small	ECOD (v295.2)
C	TrkA_N	e9yksC1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: TrkA_N	ECOD (v295.2)
B	ClpB_D2-small	e9yksB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: ClpB_D2-small	ECOD (v295.2)
A	ClpB_D2-small	e9yksA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: ClpB_D2-small	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00856	SET domain (SET)	SET domain	-	Family
A, B, C, D	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, B, C, D	Histone-lysine N-methyltransferase EHMT2	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 H3K9 methyltransferase activity histone H3K9 monomethyltransferase activity histone methyltransferase activity histone modifying activity histone H3K56 methyltransferase activity chromatin binding promoter-specific chromatin binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding 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 H1-4K26 methyltransferase activity histone H1 methyltransferase activity	peptidyl-lysine methylation protein methylation peptidyl-lysine modification primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process peptidyl-lysine dimethylation peptidyl-lysine methylation protein methylation peptidyl-lysine modification primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process peptidyl-lysine dimethylation cellular component organization organelle organization chromosome condensation chromosome organization cellular component organization or biogenesis regulation of biological process regulation of cellular process biological regulation DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process regulation of biosynthetic process epigenetic regulation of gene expression gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation negative regulation of biological process cellular component biogenesis cellular component assembly negative regulation of cellular process negative regulation of macromolecule metabolic process heterochromatin formation negative regulation of metabolic process heterochromatin organization negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR043550	Histone-lysine N-methyltransferase EHMT1/EHMT2	Family
A, B, C, D	IPR007728	Pre-SET domain	Domain
A, B, C, D	IPR046341	SET domain superfamily	Homologous Superfamily
A, B, C, D	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR001214	SET domain	Domain
A, B, C, D	IPR038034	Histone-lysine N-methyltransferase EHMT2, SET domain	Domain
A, B, C, D	IPR047762	EHMT1/2, cysteine-rich region	Domain
A, B, C, D	IPR002110	Ankyrin repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	: Q96KQ7	acute myeloid leukemia cocaine abuse Neoplasm Metastasis vesicular stomatitis cocaine dependence lung cancer non-alcoholic fatty liver disease primary hyperoxaluria type 1 age-related macular degeneration squamous cell lung carcinoma systemic lupus erythematosus vitiligo hepatitis B virus infection infertility disorder lung carcinoma acute myeloid leukemia cocaine abuse Neoplasm Metastasis vesicular stomatitis cocaine dependence lung cancer non-alcoholic fatty liver disease primary hyperoxaluria type 1 age-related macular degeneration squamous cell lung carcinoma systemic lupus erythematosus vitiligo hepatitis B virus infection infertility disorder lung carcinoma membranous glomerulonephritis osteosarcoma psoriatic arthritis ulcerative colitis wet macular degeneration endometriosis Hashimoto thyroiditis hypertensive disorder lung benign neoplasm ovarian cancer skin basal cell carcinoma autism spectrum disorder cervical cancer eosinophilic esophagitis heart disease

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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.