5NR3 | pdb_00005nr3

Human DNMT3B PWWP domain in complex with ethambutol

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)
B	d5nr3b_	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	PWWP domain	DNA methyltransferase DNMT3B	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5nr3a_	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	PWWP domain	DNA methyltransferase DNMT3B	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)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8067898	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8067898	3000404	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	PWWP	e5nr3B1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
A	PWWP	e5nr3A1	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)
B	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
B	1.10.720.50	Mainly Alpha	Orthogonal Bundle	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (utative)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
A	1.10.720.50	Mainly Alpha	Orthogonal Bundle	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	DNA (cytosine-5)-methyltransferase 3B	DNA binding binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity 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 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates DNA binding binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity 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 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process methylation 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 transcription by RNA polymerase II 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	protein-containing complex catalytic complex 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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9UBC3	immunodeficiency-centromeric instability-facial anomalies syndrome 1 primary immunodeficiency disease breast carcinoma facioscapulohumeral muscular dystrophy 2 Craniofacial Abnormalities prostate cancer sarcomatoid carcinoma carcinoma immunodeficiency-centromeric instability-facial anomalies syndrome intellectual disability lung adenocarcinoma medulloblastoma non-small cell lung carcinoma autism spectrum disorder schizophrenia immunodeficiency-centromeric instability-facial anomalies syndrome 1 primary immunodeficiency disease breast carcinoma facioscapulohumeral muscular dystrophy 2 Craniofacial Abnormalities prostate cancer sarcomatoid carcinoma carcinoma immunodeficiency-centromeric instability-facial anomalies syndrome intellectual disability lung adenocarcinoma medulloblastoma non-small cell lung carcinoma autism spectrum disorder schizophrenia hereditary diffuse gastric adenocarcinoma invasive ductal breast carcinoma malignant mesothelioma ovarian cancer primitive neuroectodermal tumor cancer undifferentiated carcinoma gastric cancer inflammatory bowel disease large cell medulloblastoma nicotine dependence polycystic ovary syndrome atypical teratoid rhabdoid tumor breast cancer gastric neoplasm

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.