5FYS

Crystal structure of the catalytic domain of human JARID1B in complex with D-2-hydroxyglutarate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d5fysa1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	Jumonji domain / Histone demethylase core	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5fysa2	Small proteins	Jumonji C-terminal domain-like	Jumonji C-terminal domain-like	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5fysa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	zf-C5HC2	e5fysA1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C5HC2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21323	Lysine-specific demethylase 5, C-terminal helical domain (KDM5_C-hel)	Lysine-specific demethylase 5, C-terminal helical domain	This is the C-terminal helical domain from Lysine-specific demethylase 5 subfamily (KDM5), which is localised between the Jumonji C (JmjC) domain and the C5HC2 zinc finger motif (Pfam:PF02928) [1-5].	Domain
A	PF02373	JmjC domain, hydroxylase (JmjC)	JmjC domain, hydroxylase	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the ...	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].	Domain
A	PF02928	C5HC2 zinc finger (zf-C5HC2)	C5HC2 zinc finger	Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji [1]. This domain may have a DNA binding function.	Domain
A	PF02375	jmjN domain (JmjN)	jmjN domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	LYSINE-SPECIFIC DEMETHYLASE 5B	binding organic cyclic compound binding nucleic acid binding protein binding histone binding DNA binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity catalytic activity, acting on a protein protein demethylase activity histone H3 demethylase activity binding organic cyclic compound binding nucleic acid binding protein binding histone binding DNA binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity catalytic activity, acting on a protein protein demethylase activity histone H3 demethylase activity histone modifying activity histone demethylase activity catalytic activity demethylase activity histone H3K4 demethylase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H3K4me/H3K4me2/H3K4me3 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen dioxygenase activity oxidoreductase activity 2-oxoglutarate-dependent dioxygenase activity sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding	regulation of cellular process 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 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 regulation of cellular process 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 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 biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process multicellular organismal process epithelium development cellular developmental process sensory organ development eye development animal organ development visual system development tissue development epithelial cell differentiation multicellular organism development cell differentiation anatomical structure development camera-type eye development lens fiber cell differentiation sensory system development lens development in camera-type eye system development positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of localization system process regulation of hormone secretion transport signaling steroid hormone secretion regulation of system process regulation of lipid transport organic hydroxy compound transport estradiol secretion hormone secretion cell communication regulation of estradiol secretion localization secretion by cell regulation of steroid hormone secretion regulation of secretion by cell signal release regulation of multicellular organismal process regulation of biological quality regulation of signaling secretion regulation of transport regulation of hormone levels lipid localization export from cell cell-cell signaling lipid transport establishment of localization regulation of secretion endocrine hormone secretion endocrine process regulation of lipid localization lipid export from cell macromolecule localization hormone transport regulation of cell communication regulation of endocrine process reproductive system development reproductive process uterus development developmental process involved in reproduction uterus morphogenesis anatomical structure morphogenesis reproductive structure development animal organ morphogenesis sexual reproduction fertilization single fertilization response to fibroblast growth factor cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus response to growth factor cellular response to fibroblast growth factor stimulus developmental growth mammary gland morphogenesis mammary gland development gland development tube morphogenesis gland morphogenesis mammary duct terminal end bud growth epithelial tube morphogenesis tube development growth morphogenesis of an epithelium developmental growth involved in morphogenesis mammary gland duct morphogenesis tissue morphogenesis mammary gland epithelium development rhythmic process response to chemical response to antibiotic response to fungicide response to toxic substance regulation of developmental process positive regulation of cell population proliferation positive regulation of mammary gland epithelial cell proliferation positive regulation of developmental process epithelial cell proliferation cell population proliferation positive regulation of epithelial cell proliferation regulation of mammary gland epithelial cell proliferation regulation of cell population proliferation positive regulation of multicellular organismal process regulation of epithelial cell proliferation mammary gland epithelial cell proliferation branching involved in mammary gland duct morphogenesis branching morphogenesis of an epithelial tube morphogenesis of a branching structure morphogenesis of a branching epithelium post-embryonic development response to peptide response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR048615	Lysine-specific demethylase 5, C-terminal helical domain	Domain
A	IPR003347	JmjC domain	Domain
A	IPR003349	JmjN domain	Domain
A	IPR001606	ARID DNA-binding domain	Domain
A	IPR047981	Lysine-specific demethylase 5B, ARID domain	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR047978	Lysine-specific demethylase 5B, first PHD-finger	Domain
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR013637	Lysine-specific demethylase-like domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR004198	Zinc finger, C5HC2-type	Domain
A	IPR036431	ARID DNA-binding domain superfamily	Homologous Superfamily
A	IPR047979	Lysine-specific demethylase 5B, third PHD-finger	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9UGL1	malignant colon neoplasm autism spectrum disorder ductal breast carcinoma in situ lung adenocarcinoma malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor benign colon neoplasm intellectual disability lung cancer malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm spina bifida malignant colon neoplasm autism spectrum disorder ductal breast carcinoma in situ lung adenocarcinoma malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor benign colon neoplasm intellectual disability lung cancer malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm spina bifida colonic neoplasm invasive ductal breast carcinoma medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.