5YLT | pdb_00005ylt

Crystal structure of SET7/9 in complex with a cyproheptadine derivative

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5ylta1	All beta proteins	open-sided beta-meander	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5ylta2	All beta proteins	beta-clip	SET domain	Histone lysine methyltransferases	Histone H3 K4-specific methyltransferase SET7/9 catalytic domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SET domain	8042399	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	bZIP_1	e5yltA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: bZIP_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.20.110.10	Mainly Beta	Single Sheet	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal 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	PF00856	SET domain (SET)	SET domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Histone-lysine N-methyltransferase SETD7	p53 binding protein binding 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 p53 binding protein binding 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 modifying activity histone methyltransferase activity chromatin binding histone H3K4 monomethyltransferase activity histone H3K4 methyltransferase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process peptidyl-lysine methylation protein methylation peptidyl-lysine modification primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process peptidyl-lysine methylation protein methylation peptidyl-lysine modification primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process peptidyl-lysine dimethylation regulation of cellular process regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process regulation of response to stress negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process DNA repair negative regulation of macromolecule metabolic process regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process biological regulation DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of response to stimulus negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process response to alcohol response to chemical response to oxygen-containing compound response to ethanol peptidyl-lysine monomethylation cellular component organization chromatin organization heterochromatin organization cellular component organization or biogenesis positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nucleoplasm chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR046341	SET domain superfamily	Homologous Superfamily
A	IPR017155	Histone-lysine N-methyltransferase SETD7	Family
A	IPR001214	SET domain	Domain
A	IPR054533	Histone-lysine methyltransferase SETD7, N-terminal	Domain
A	IPR044436	SETD7, SET domain	Domain
A	IPR003409	MORN repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8WTS6	atypical teratoid rhabdoid tumor malignant ependymoma pituitary cancer Crohn disease ovarian cancer ulcerative colitis invasive ductal breast carcinoma pancreatic ductal adenocarcinoma

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.