2RFI | pdb_00002rfi

Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 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)
B	SCOP2B Superfamily	SET domain	8004150	3000162	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CXC domain-like	8091567	3002037	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CXC domain-like	8091567	3002037	SCOP2B (2022-06-29)
A	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)
B	DAO	e2rfiB2	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (v294.1)
B	LepA_C	e2rfiB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: LepA_C	ECOD (v294.1)
A	DAO	e2rfiA2	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: DAO	ECOD (v294.1)
A	LepA_C	e2rfiA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: LepA_C	ECOD (v294.1)

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
A, B	Histone-lysine N-methyltransferase, H3 lysine-9 specific 5	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
C [auth P], D [auth Q]	Histone H3	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR047762	EHMT1/2, cysteine-rich region	Domain
A, B	IPR002110	Ankyrin repeat	Repeat
A, B	IPR038035	Histone-lysine N-methyltransferase EHMT1, SET domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, 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
C [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.