5T0K | pdb_00005t0k

Structure of G9a SET-domain with H3K9M mutant peptide and SAM

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)
B	SCOP2B Superfamily	SET domain	8088641	3000162	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CXC domain-like	8092240	3002037	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)
B	Ribosomal_L5,Ribosomal_L5_C	e5t0kB1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L5,Ribosomal_L5_C	ECOD (develop294)
A	Ribosomal_L5,Ribosomal_L5_C	e5t0kA1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L5,Ribosomal_L5_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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, B	PF00856	SET domain (SET)	SET domain	-	Family
A, 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
C [auth P], D [auth Q]	H3K9 mutant peptide	DNA binding binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization telomere organization chromosome organization regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B	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	developmental process multicellular organismal process cellular developmental process neuron fate commitment nervous system development cell fate specification generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development cellular process neuron fate specification developmental process multicellular organismal process cellular developmental process neuron fate commitment nervous system development cell fate specification generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development cellular process neuron fate specification cell fate commitment system development behavior adult behavior response to stimulus behavioral response to cocaine response to chemical response to oxygen-containing compound response to nitrogen compound response to cocaine response to alkaloid regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization 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 epigenetic regulation of gene expression negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule 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 macromolecule metabolic process regulation of metabolic process developmental growth growth organ growth sexual reproduction reproductive process fertilization peptidyl-lysine methylation protein methylation peptidyl-lysine modification primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process peptidyl-lysine dimethylation meiotic chromosome segregation synaptonemal complex assembly meiotic cell cycle process cellular component biogenesis cellular component assembly meiosis I meiotic nuclear division cell cycle synaptonemal complex organization chromosome segregation cell cycle process meiotic cell cycle organelle fission chromosome organization chromosome organization involved in meiotic cell cycle organelle organization nuclear division meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation chromosome condensation DNA 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 DNA replication regulation of DNA metabolic process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation oocyte development germ cell development oocyte differentiation phenotypic switching cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to stress response to stress response to starvation cellular response to starvation heterochromatin formation heterochromatin organization constitutive heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation spermatid development spermatid differentiation spermatogenesis male gamete generation cellular response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to cocaine cellular response to alkaloid catabolic process regulation of cellular component organization macroautophagy autophagy negative regulation of organelle assembly autophagosome organization regulation of autophagy process utilizing autophagic mechanism negative regulation of autophagosome assembly negative regulation of catabolic process autophagosome assembly organelle assembly vacuole organization negative regulation of cellular component organization regulation of autophagosome assembly regulation of vacuole organization regulation of catabolic process regulation of cellular component biogenesis regulation of organelle organization negative regulation of macroautophagy regulation of macroautophagy negative regulation of organelle organization negative regulation of autophagy regulation of organelle assembly 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
C [auth P], D [auth Q]	IPR009072	Histone-fold	Homologous Superfamily
C [auth P], D [auth Q]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C [auth P], D [auth Q]	IPR000164	Histone H3/CENP-A	Family
A, B	IPR043550	Histone-lysine N-methyltransferase EHMT1/EHMT2	Family
A, B	IPR007728	Pre-SET domain	Domain
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR001214	SET domain	Domain
A, B	IPR038034	Histone-lysine N-methyltransferase EHMT2, SET domain	Domain
A, B	IPR047762	EHMT1/2, cysteine-rich region	Domain
A, B	IPR002110	Ankyrin repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth P], D [auth Q]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pancreatic intraductal papillary-mucinous carcinoma astrocytoma (excluding glioblastoma) spina bifida breast cancer cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor subependymoma breast carcinoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
A, B	Pharos: Q96KQ7	acute myeloid leukemia cocaine abuse Neoplasm Metastasis vesicular stomatitis cocaine dependence lung cancer non-alcoholic fatty liver disease primary hyperoxaluria type 1 squamous cell lung carcinoma age-related macular degeneration 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 squamous cell lung carcinoma age-related macular degeneration 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

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.