3KV5 | pdb_00003kv5

Structure of KIAA1718, human Jumonji demethylase, in complex with N-oxalylglycine

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 [auth A]		e3kv5A1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: MCM_OB	F:	ECOD (20:10:01)
A [auth D]		e3kv5D1	A: amino-terminal domain of OmpATb	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: MCM_OB	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B [auth A]	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
B [auth A]	1.20.58.1360	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A [auth D]	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A [auth D]	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
A [auth D]	1.20.58.1360	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth A]	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain
A [auth D], B [auth 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 [auth D], B [auth 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
A [auth D], B [auth A]	JmjC domain-containing histone demethylation protein 1D	transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor 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 transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor 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 histone H3K9me/H3K9me2 demethylase activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity histone H3K36 demethylase activity histone H4 demethylase activity histone H4K20 demethylase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding histone H3K27me2/H3K27me3 demethylase activity zinc ion binding	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 regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological 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 regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological 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 positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth A]	IPR001965	Zinc finger, PHD-type	Domain
A [auth D], B [auth A]	IPR003347	JmjC domain	Domain
A [auth D], B [auth A]	IPR041070	Jumonji, helical domain	Domain
A [auth D], B [auth A]	IPR019787	Zinc finger, PHD-finger	Domain
A [auth D], B [auth A]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A [auth D], B [auth A]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A [auth D], B [auth A]	IPR050690	JHDM1 Histone Demethylase	Family
A [auth D], B [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D], B [auth A]	Pharos: Q6ZMT4	amyotrophic lateral sclerosis invasive ductal breast carcinoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia diabetes mellitus lung cancer myocardial infarction pancreatic intraductal papillary-mucinous carcinoma psoriasis heart disease MALT lymphoma myopathy pancreatic intraductal papillary-mucinous neoplasm

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.