4O64

Zinc fingers of KDM2B

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PHD domain	8046271	4003778	SCOP2 (2022-06-29)
A	SCOP2 Family	CXXC zinc-finger domain	8049709	4006601	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FYVE/PHD zinc finger	8053014	3001459	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CXXC zinc-finger domain	8053013	3002156	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	FYVE/PHD zinc finger	8053014	3001459	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CXXC zinc-finger domain	8053013	3002156	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FYVE/PHD zinc finger	8053014	3001459	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CXXC zinc-finger domain	8053013	3002156	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	zf-CXXC	e4o64A1	A: few secondary structure elements	X: CXXC domain-like	H: CXXC domain (From Topology)	T: CXXC domain	F: zf-CXXC	ECOD (1.6)
A	PHD_5	e4o64A2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)
C	zf-CXXC	e4o64C2	A: few secondary structure elements	X: CXXC domain-like	H: CXXC domain (From Topology)	T: CXXC domain	F: zf-CXXC	ECOD (1.6)
C	PHD_5	e4o64C1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)
B	zf-CXXC	e4o64B2	A: few secondary structure elements	X: CXXC domain-like	H: CXXC domain (From Topology)	T: CXXC domain	F: zf-CXXC	ECOD (1.6)
B	PHD_5	e4o64B1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF02008	CXXC zinc finger domain (zf-CXXC)	CXXC zinc finger domain	This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [ ...	This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [3], and shows a peculiar internal duplication in which the second unit is inserted into the first one [4]. Each of these units is characterised by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR [3]. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins [4]. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases [4].	Domain
A, B, C	PF16866	PHD-finger (PHD_4)	PHD-finger	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Lysine-specific demethylase 2B	histone H3K36 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity histone H3K36me/H3K36me2 demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity RNA binding histone H3K36 demethylase activity catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity histone H3K36me/H3K36me2 demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding unmethylated CpG binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development midbrain development anatomical structure development system development spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation hindbrain development fourth ventricle development ventricular system development regulation of developmental process regulation of stem cell population maintenance stem cell population maintenance positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process regulation of multicellular organismal process maintenance of cell number lateral ventricle development forebrain development telencephalon development embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium tissue development anatomical structure morphogenesis tissue morphogenesis initiation of neural tube closure neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process third ventricle development sensory organ development embryonic eye morphogenesis visual system development embryonic camera-type eye development eye morphogenesis animal organ morphogenesis embryonic organ development sensory system development embryonic organ morphogenesis camera-type eye morphogenesis eye development embryonic camera-type eye morphogenesis sensory organ morphogenesis camera-type eye development cellular biosynthetic process RNA metabolic process regulation of primary metabolic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process negative regulation of cell population proliferation negative regulation of neural precursor cell proliferation cell population proliferation regulation of cell population proliferation neural precursor cell proliferation regulation of neural precursor cell proliferation protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling midbrain-hindbrain boundary morphogenesis anterior/posterior pattern specification pattern specification process rostrocaudal neural tube patterning regionalization neural tube patterning midbrain-hindbrain boundary development	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nucleoplasm chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR001965	Zinc finger, PHD-type	Domain
A, B, C	IPR001810	F-box domain	Domain
A, B, C	IPR003347	JmjC domain	Domain
A, B, C	IPR041070	Jumonji, helical domain	Domain
A, B, C	IPR041667	Cupin-like domain 8	Domain
A, B, C	IPR002857	Zinc finger, CXXC-type	Domain
A, B, C	IPR019787	Zinc finger, PHD-finger	Domain
A, B, C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B, C	IPR006553	Leucine-rich repeat, cysteine-containing subtype	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q8NHM5	schizophrenia adrenal cortex carcinoma medulloblastoma bipolar disorder osteosarcoma endogenous depression ovarian cancer

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.