3BO5 | pdb_00003bo5

Crystal structure of methyltransferase domain of human Histone-lysine N-methyltransferase SETMAR

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	d3bo5a_	All beta proteins	beta-clip	SET domain	automated matches	automated matches	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	SCOP2 Family	Histone lysine methyltransferases	8088644	4000376	SCOP2 (2022-06-29)
A	SCOP2 Family	preSET domain-like	8092246	4007508	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SET domain	8088645	3000162	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CXC domain-like	8092247	3002037	SCOP2 (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	SET	e3bo5A1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET	ECOD (1.6)
A	Pre-SET	e3bo5A2	A: few secondary structure elements	X: Zn3Cys9 preSET domain-related (From Topology)	H: Zn3Cys9 preSET domain-related (From Topology)	T: Zn3Cys9 preSET domain-related	F: Pre-SET	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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
A	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	Histone-lysine N-methyltransferase SETMAR	DNA topoisomerase binding protein binding binding enzyme binding protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein histone H3K36 dimethyltransferase activity transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K36 methyltransferase activity lysine N-methyltransferase activity DNA topoisomerase binding protein binding binding enzyme binding protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein histone H3K36 dimethyltransferase activity transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K36 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity DNA binding nucleic acid binding histone H3K4 methyltransferase activity double-stranded DNA binding identical protein binding protein homodimerization activity protein dimerization activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity single-stranded DNA endodeoxyribonuclease activity DNA nuclease activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding single-stranded DNA binding	catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus double-strand break repair catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing cellular response to stress DNA damage response response to stress DNA repair DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA replication replication fork processing regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process regulation of primary metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of double-strand break repair via nonhomologous end joining regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of double-strand break repair via nonhomologous end joining double-strand break repair via nonhomologous end joining biological regulation regulation of macromolecule metabolic process positive regulation of double-strand break repair regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process cell population proliferation methylation regulation of cellular component organization negative regulation of cellular component organization negative regulation of biological process chromosome organization regulation of chromosome organization regulation of organelle organization cellular component organization organelle organization negative regulation of chromosome organization negative regulation of organelle organization negative regulation of cellular process cellular component organization or biogenesis regulation of cell cycle phase transition signaling negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling mitotic cell cycle process DNA integration positive regulation of molecular function regulation of molecular function regulation of ATP-dependent activity positive regulation of ATP-dependent activity regulation of catalytic activity positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity positive regulation of catalytic activity	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 site of double-strand break site of DNA damage chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR007728	Pre-SET domain	Domain
A	IPR046341	SET domain superfamily	Homologous Superfamily
A	IPR001214	SET domain	Domain
A	IPR001888	Transposase, type 1	Family
A	IPR003616	Post-SET domain	Domain
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR052709	Transposase-Methyltransferase Hybrid	Family
A	IPR041426	Mos1 transposase, HTH domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q53H47	atypical teratoid rhabdoid tumor malignant ependymoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm breast cancer malignant glioma osteosarcoma psoriasis large cell medulloblastoma malignant mesothelioma ovarian cancer

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.