4EZH

the crystal structure of KDM6B bound with H3K27me3 peptide

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_1	e4ezhA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: JmjC_1	ECOD (1.6)
A	KOG1246_2nd	e4ezhA2	A: alpha bundles	X: C-terminal helical domain in Jumonji domain-containing histone demethylases (From Topology)	H: C-terminal helical domain in Jumonji domain-containing histone demethylases (From Topology)	T: C-terminal helical domain in Jumonji domain-containing histone demethylases	F: KOG1246_2nd	ECOD (1.6)
A	KOG1246_3rd	e4ezhA3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: KOG1246_3rd	ECOD (1.6)
B	JmjC_1	e4ezhB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: JmjC_1	ECOD (1.6)
B	KOG1246_2nd	e4ezhB3	A: alpha bundles	X: C-terminal helical domain in Jumonji domain-containing histone demethylases (From Topology)	H: C-terminal helical domain in Jumonji domain-containing histone demethylases (From Topology)	T: C-terminal helical domain in Jumonji domain-containing histone demethylases	F: KOG1246_2nd	ECOD (1.6)
B	KOG1246_3rd	e4ezhB2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: KOG1246_3rd	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)
A	1.20.58.1370	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	2.10.110.20	Mainly Beta	Ribbon	Cysteine Rich Protein		CATH (4.3.0)
B	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
B	1.20.58.1370	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	2.10.110.20	Mainly Beta	Ribbon	Cysteine Rich Protein		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21322	Lysine-specific demethylase 6/UTY, C-terminal helical domain (KDM6_C-hel)	Lysine-specific demethylase 6/UTY, C-terminal helical domain	Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry incudes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also ...	Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry incudes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also known as JMJD3) and the related histone demethylase UTY [[1-4]. This is the C-terminal helical domain localised adjacent the JmjC domain.	Domain
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	PF21326	KDM6, GATA-like (KDM6_GATAL)	KDM6, GATA-like	Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry includes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also ...	Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry includes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also known as JMJD3) and the related histone demethylase UTY (also known as KMD6C) [1,2]. This entry represents the Zn2+-coordinated GATA-like (GATAL) domain [1,2], which seems to be sensitive to redox environment. It is involved in substrate binding [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Lysine-specific demethylase 6B	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding chromatin DNA binding DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding chromatin DNA binding 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 demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity histone H3K27me2/H3K27me3 demethylase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity beta-catenin binding protein binding cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development multicellular organism development central nervous system development anatomical structure development telencephalon development hippocampus development limbic system development developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development multicellular organism development central nervous system development anatomical structure development telencephalon development hippocampus development limbic system development system development regulation of biosynthetic process regulation of biological process regulation of cellular process cellular biosynthetic process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process response to stimulus response to activity heart development cellular developmental process cardiac muscle tissue development cardiac muscle cell differentiation muscle cell differentiation tissue development cardiocyte differentiation striated muscle tissue development circulatory system development muscle structure development cell differentiation striated muscle cell differentiation muscle tissue development epithelium development endothelial cell differentiation endothelium development epithelial cell differentiation cellular response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress response to stress response to chemical homeostatic process positive regulation of biological process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process regulation of multicellular organismal process defense response immune response immune system process inflammatory response inflammatory response to antigenic stimulus response to antibiotic response to fungicide response to toxic substance cell fate commitment formation of primary germ layer mesodermal cell differentiation mesoderm morphogenesis embryonic morphogenesis embryo development gastrulation tissue morphogenesis anatomical structure morphogenesis anatomical structure formation involved in morphogenesis mesoderm formation mesoderm development positive regulation of DNA-templated transcription RNA metabolic process positive regulation of cellular 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 DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II 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 transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription positive regulation of cellular biosynthetic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle MLL3/4 complex protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex intracellular organelle lumen intracellular organelle membrane-bounded organelle MLL3/4 complex protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen
C, D	SYNTHESIZED methylation 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR048562	Lysine-specific demethylase 6A/B-like, C-terminal helical domain	Domain
A, B	IPR003347	JmjC domain	Domain
A, B	IPR046941	Lysine-specific demethylase 6, GATA-like domain superfamily	Homologous Superfamily
A, B	IPR048560	Lysine-specific demethylase 6A/B-like, GATA-like	Domain
A, B	IPR051630	Transcriptional Corepressor and Histone Demethylase	Family
C, D	IPR009072	Histone-fold	Homologous Superfamily
C, D	IPR007125	Histone H2A/H2B/H3	Domain
C, D	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	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.