6BP4

Structure of the S. pombe Clr4 catalytic domain bound to 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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	CXC domain-like	8051804	3002037	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	SET domain	8043806	3000162	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	CXC domain-like	8051804	3002037	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	SET domain	8043806	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 [auth B]	PF00856	e6bp4B1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: PF00856	ECOD (1.6)
A [auth B]	PF05033	e6bp4B2	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: PF05033	ECOD (1.6)
B [auth A]	PF00856	e6bp4A2	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: PF00856	ECOD (1.6)
B [auth A]	PF05033	e6bp4A1	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: PF05033	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
B [auth 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 [auth B], B [auth A]	PF00856	SET domain (SET)	SET domain	-	Family
A [auth B], B [auth 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 [auth B], B [auth A]	Histone-lysine N-methyltransferase, H3 lysine-9 specific	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 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 RNA binding binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding protein binding ubiquitin binding ubiquitin-like protein binding histone H3K9me2 methyltransferase activity DNA binding double-stranded DNA binding histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity modification-dependent protein binding ubiquitin-like protein reader activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding single-stranded DNA binding	positive regulation of organelle organization regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process cellular component biogenesis chromatin organization organic substance biosynthetic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of chromosome organization positive regulation of organelle organization regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process cellular component biogenesis chromatin organization organic substance biosynthetic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of chromosome organization negative regulation of cellular biosynthetic process regulation of organelle organization positive regulation of chromosome organization regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation 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 regulation of cellular component organization positive regulation of cellular component organization cellular biosynthetic process positive regulation of biological process protein-DNA complex organization cellular component organization positive regulation of heterochromatin formation organic substance metabolic process regulation of pericentric heterochromatin formation negative regulation of cellular process chromatin remodeling positive regulation of chromatin organization cellular component organization or biogenesis positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process positive regulation of pericentric heterochromatin formation heterochromatin formation protein-containing complex organization positive regulation of cellular component biogenesis epigenetic regulation of gene expression biological regulation chromosome organization regulation of macromolecule metabolic process gene expression regulation of cellular component biogenesis macromolecule biosynthetic process regulation of cellular biosynthetic process pericentric heterochromatin formation organelle organization negative regulation of biosynthetic process cellular process siRNA-mediated pericentric heterochromatin formation regulatory ncRNA-mediated gene silencing regulatory ncRNA-mediated heterochromatin formation methylation silent mating-type cassette heterochromatin formation	protein-containing complex intracellular anatomical structure protein-DNA complex mating-type region heterochromatin chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle ubiquitin ligase complex protein-containing complex intracellular anatomical structure protein-DNA complex mating-type region heterochromatin chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle ubiquitin ligase complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen CLRC complex cullin-RING ubiquitin ligase complex nucleoplasm methyltransferase complex histone methyltransferase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex intracellular membrane-bounded organelle nuclear ubiquitin ligase complex organelle lumen intracellular protein-containing complex nuclear lumen cytoplasm chromosome, subtelomeric region chromosome, telomeric region chromosomal region pericentric heterochromatin chromosome, centromeric region microtubule organizing center cytoskeleton spindle pole body microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A]	IPR007728	Pre-SET domain	Domain
A [auth B], B [auth A]	IPR046341	SET domain superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR023780	Chromo domain	Domain
A [auth B], B [auth A]	IPR001214	SET domain	Domain
A [auth B], B [auth A]	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR023779	Chromo domain, conserved site	Conserved Site
A [auth B], B [auth A]	IPR011381	Histone-lysine N-methyltransferase SUV39H1/2-like	Family
A [auth B], B [auth A]	IPR003616	Post-SET domain	Domain
A [auth B], B [auth A]	IPR000953	Chromo/chromo shadow domain	Domain

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 R01GM133198.