Annotations: 1KHC

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1khca_	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	PWWP domain	DNA methyltransferase DNMT3B	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PWWP domain	8025852	4003064	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Tudor/PWWP/MBT domain-like	8038231	3000404	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	PWWP	e1khcA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	1.10.720.50	Mainly Alpha	Orthogonal Bundle	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00855	PWWP domain (PWWP)	PWWP domain	The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif [1]. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic c ...	The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif [1]. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyses all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organising higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA cytosine-5 methyltransferase 3B2	RNA binding binding lncRNA binding nucleic acid binding DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates RNA binding binding lncRNA binding nucleic acid binding DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates DNA binding DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates cation binding ion binding metal ion binding small molecule binding	methylation metabolic process cellular process 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 cellular component organization regulation of gene expression biosynthetic process methylation metabolic process cellular process 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 cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process cellular component organization or biogenesis macromolecule metabolic process regulation of metabolic process localization protein-containing complex localization negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process heterochromatin formation negative regulation of metabolic process regulatory ncRNA-mediated gene silencing negative regulation of gene expression constitutive heterochromatin formation regulatory ncRNA-mediated heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process DNA methylation-dependent constitutive heterochromatin formation gene silencing by piRNA-directed DNA methylation piRNA-mediated heterochromatin formation negative regulation of gene expression, epigenetic retrotransposition transposable element silencing by heterochromatin formation transposition transposable element silencing sexual reproduction cellular developmental process reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation cell differentiation anatomical structure development developmental process epigenetic programming of gene expression multicellular organismal reproductive process genomic imprinting autosome genomic imprinting germ cell development cellular response to acid chemical cellular response to stimulus cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to stimulus response to chemical response to amino acid 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 transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process 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 primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle chromosome, centromeric region intracellular membraneless organelle chromosome chromosomal region membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle chromosome, centromeric region intracellular membraneless organelle chromosome chromosomal region membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin heterochromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR040552	DNMT3, cysteine rich ADD domain, GATA1-like zinc finger	Domain
A	IPR000313	PWWP domain	Domain
A	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR049554	DNMT3, ADD domain, PHD zinc finger	Domain
A	IPR030488	DNA (cytosine-5)-methyltransferase 3B, ADD domain	Domain
A	IPR001525	C-5 cytosine methyltransferase	Family
A	IPR025766	ADD 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 R01GM157729.