4HON

Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and 2-oxoglutarate

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	JmjC	e4honA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: JmjC	ECOD (1.6)
B	JmjC	e4honB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: JmjC	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)
B	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, B	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, B	PF02375	jmjN domain (JmjN)	jmjN domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth F], D [auth G]	Histone H3 Peptide	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization biosynthetic process protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization biosynthetic process cellular biosynthetic process cellular metabolic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B	Lysine-specific demethylase 4D	histone H3K9me2/H3K9me3 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 H3K9 demethylase activity histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity DNA binding histone H3K9me2/H3K9me3 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 H3K9 demethylase activity histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity DNA binding binding chromatin binding organic cyclic compound binding nucleic acid binding chromatin DNA binding damaged DNA binding cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process regulation of primary metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of double-strand break repair via nonhomologous end joining regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of double-strand break repair via nonhomologous end joining double-strand break repair via nonhomologous end joining biological regulation regulation of macromolecule metabolic process positive regulation of double-strand break repair regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process regulation of protein modification process regulation of protein phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process cellular metabolic process regulation of cellular metabolic process macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process regulation of biosynthetic process cellular biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process defense response inflammatory response response to ionizing radiation cellular response to ionizing radiation response to radiation response to abiotic stimulus cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus positive regulation of chromatin binding regulation of molecular function positive regulation of molecular function regulation of binding regulation of chromatin binding positive regulation of binding cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	extracellular region extracellular space cellular anatomical entity blood microparticle intracellular organelle site of double-strand break intracellular anatomical structure organelle intracellular non-membrane-bounded organelle site of DNA damage chromosome non-membrane-bounded organelle membrane-bounded organelle nucleus extracellular region extracellular space cellular anatomical entity blood microparticle intracellular organelle site of double-strand break intracellular anatomical structure organelle intracellular non-membrane-bounded organelle site of DNA damage chromosome non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin pericentric heterochromatin heterochromatin chromosomal region chromosome, centromeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth F], D [auth G]	IPR009072	Histone-fold	Homologous Superfamily
C [auth F], D [auth G]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth F], D [auth G]	IPR000164	Histone H3/CENP-A	Family
A, B	IPR003347	JmjC domain	Domain
A, B	IPR003349	JmjN domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth F], D [auth G]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
A, B	Pharos: Q6B0I6	large cell medulloblastoma malignant mesothelioma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth F], D [auth G]	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.