6F4P | pdb_00006f4p

Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1)

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)
A	TIP49_C	e6f4pA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: TIP49_C	ECOD (v294.1)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B	40S ribosomal protein S6	RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome mRNA binding protein binding kinase binding enzyme binding protein kinase binding	regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process cellular process apoptotic process programmed cell death positive regulation of cellular process ribonucleoprotein complex biogenesis regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process cellular process apoptotic process programmed cell death positive regulation of cellular process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process bicellular tight junction assembly regulation of cellular component organization negative regulation of biological process tight junction organization cellular component organization cellular component assembly negative regulation of cell junction assembly cell junction assembly negative regulation of cellular process cell-cell junction assembly cell-cell junction organization regulation of bicellular tight junction assembly negative regulation of cellular component organization apical junction assembly regulation of cellular component biogenesis regulation of cell junction assembly cell junction organization tight junction assembly negative regulation of bicellular tight junction assembly cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation translation protein biosynthetic process cytoplasmic translation protein metabolic process cellular response to stimulus response to stimulus response to alcohol response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to chemical cellular response to ethanol response to ethanol response to hormone response to endogenous stimulus response to peptide hormone response to insulin response to nitrogen compound ribosomal small subunit biogenesis TOR signaling signaling intracellular signal transduction cell communication signal transduction organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly organelle organization protein-RNA complex organization protein-containing complex assembly ribosome assembly chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis	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 membrane cytoplasm cytosol presynapse synapse cell junction somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection nucleoplasm GABA-ergic synapse cytoplasmic ribonucleoprotein granule supramolecular complex ribonucleoprotein granule protein-containing complex small ribosomal subunit ribosomal subunit ribonucleoprotein complex ribosome cytosolic ribosome preribosome nuclear protein-containing complex small-subunit processome cell body cytosolic small ribosomal subunit endoplasmic reticulum endomembrane system
A	JmjC domain-containing protein 5	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
B	IPR018282	Small ribosomal subunit protein eS6, conserved site	Conserved Site
B	IPR001377	Small ribosomal subunit protein eS6	Family
B	IPR014401	Small ribosomal subunit protein eS6-like	Family
A	IPR056520	KDM8, N-terminal	Domain
A	IPR003347	JmjC domain	Domain
A	IPR041667	Cupin-like domain 8	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P62753	breast carcinoma breast cancer Disease Progression hepatocellular carcinoma lung cancer gastric cancer hereditary diffuse gastric adenocarcinoma gastric neoplasm pancreatic intraductal papillary-mucinous neoplasm
A	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.