9PHV | pdb_00009phv

Crystal structure of human KDM2A with substrate competitive inhibitor 183c

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF17811	Jumonji helical domain (JHD)	Jumonji helical domain	This 4-helix bundle domain is associated with the Jumonji domain Pfam:PF02373 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D]	Lysine-specific demethylase 2A	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 transcription regulator activity 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 transcription regulator activity transcription coregulator activity sequence-specific DNA binding DNA binding binding unmethylated CpG binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	rhythmic process regulation of biological process circadian rhythm biological regulation regulation of circadian rhythm catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process rhythmic process regulation of biological process circadian rhythm biological regulation regulation of circadian rhythm catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process regulation of biosynthetic process regulation of cellular process circadian regulation of gene expression regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process regulation of primary metabolic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	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 membraneless organelle intracellular membraneless organelle 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 membraneless organelle intracellular membraneless organelle chromosome
A	Lysine-specific demethylase 2A	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 transcription regulator activity 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 transcription regulator activity transcription coregulator activity sequence-specific DNA binding DNA binding binding unmethylated CpG binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	rhythmic process regulation of biological process circadian rhythm biological regulation regulation of circadian rhythm catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process rhythmic process regulation of biological process circadian rhythm biological regulation regulation of circadian rhythm catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process regulation of biosynthetic process regulation of cellular process circadian regulation of gene expression regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process regulation of primary metabolic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	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 membraneless organelle intracellular membraneless organelle 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 membraneless organelle intracellular membraneless organelle chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D]	IPR001965	Zinc finger, PHD-type	Domain
B [auth D]	IPR001810	F-box domain	Domain
B [auth D]	IPR003347	JmjC domain	Domain
B [auth D]	IPR041070	Jumonji, helical domain	Domain
B [auth D]	IPR002857	Zinc finger, CXXC-type	Domain
B [auth D]	IPR019787	Zinc finger, PHD-finger	Domain
B [auth D]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B [auth D]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
B [auth D]	IPR050690	JHDM1 Histone Demethylase	Family
B [auth D]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth D]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
B [auth D]	IPR006553	Leucine-rich repeat, cysteine-containing subtype	Repeat
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR001810	F-box domain	Domain
A	IPR003347	JmjC domain	Domain
A	IPR041070	Jumonji, helical domain	Domain
A	IPR002857	Zinc finger, CXXC-type	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR050690	JHDM1 Histone Demethylase	Family
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A	IPR006553	Leucine-rich repeat, cysteine-containing subtype	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth D]	: Q9Y2K7	colorectal cancer astrocytic tumor Colorectal Neoplasms osteosarcoma dermatomyositis ovarian cancer prostate carcinoma colorectal carcinoma juvenile dermatomyositis pancreatic ductal adenocarcinoma psoriasis
A	: Q9Y2K7	colorectal cancer astrocytic tumor Colorectal Neoplasms osteosarcoma dermatomyositis ovarian cancer prostate carcinoma colorectal carcinoma juvenile dermatomyositis pancreatic ductal adenocarcinoma psoriasis

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.