4AAP | pdb_00004aap

Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG)

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Cupin_2	e4aapB2	A: alpha bundles	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: Cupin_2	ECOD (develop294)
A	Ras	e4aapA1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Ras	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
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, B	PF13621	Cupin-like domain (Cupin_8)	Cupin-like domain	This cupin like domain shares similarity to the JmjC domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	LYSINE-SPECIFIC DEMETHYLASE 8	p53 binding protein binding binding oxidoreductase activity peptidyl-arginine 3-dioxygenase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity histone H3K36 demethylase activity protein demethylase activity histone demethylase activity demethylase activity p53 binding protein binding binding oxidoreductase activity peptidyl-arginine 3-dioxygenase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity histone H3K36 demethylase activity protein demethylase activity histone demethylase activity demethylase activity histone H3 demethylase activity histone modifying activity peptidase activity hydrolase activity endopeptidase activity chromatin binding cation binding ion binding metal ion binding small molecule binding aminopeptidase activity exopeptidase activity	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 fibroblast proliferation cell population proliferation protein destabilization regulation of protein stability regulation of biological quality positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cellular response to stimulus regulation of signaling response to stimulus signaling regulation of signal transduction signal transduction by p53 class mediator intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus regulation of signal transduction by p53 class mediator regulation of cell communication signal transduction cell cycle G2/M phase transition mitotic cell cycle process G2/M transition of mitotic cell cycle cell cycle phase transition cell cycle mitotic cell cycle cell cycle process mitotic cell cycle phase transition proteolysis protein metabolic process rhythmic process circadian regulation of gene expression circadian rhythm developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR056520	KDM8, N-terminal	Domain
A, B	IPR003347	JmjC domain	Domain
A, B	IPR041667	Cupin-like domain 8	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8N371	hepatocellular carcinoma pancreatic ductal adenocarcinoma peripheral arterial disease

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.

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