6MEV | pdb_00006mev

Structure of JMJD6 bound to Mono-Methyl Arginine.

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)
H	V-set	e6mevH1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: V-set	ECOD (v295.2)
G	V-set	e6mevG1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: V-set	ECOD (v295.2)
F	V-set	e6mevF1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: V-set	ECOD (v295.2)
E	V-set	e6mevE1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: V-set	ECOD (v295.2)
D	V-set	e6mevD1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: V-set	ECOD (v295.2)
C	V-set	e6mevC1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: V-set	ECOD (v295.2)
B	V-set	e6mevB1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: V-set	ECOD (v295.2)
A	MAM33	e6mevA1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: MAM33	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (utative)
H	1.20.1280.270	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (utative)
G	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (utative)
G	1.20.1280.270	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (utative)
F	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (utative)
F	1.20.1280.270	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (utative)
E	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (utative)
E	1.20.1280.270	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (utative)
D	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (utative)
D	1.20.1280.270	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (utative)
C	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (utative)
C	1.20.1280.270	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (utative)
B	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (utative)
B	1.20.1280.270	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (utative)
A	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (utative)
A	1.20.1280.270	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6	molecular transducer activity signaling receptor activity protein demethylase activity catalytic activity, acting on a protein catalytic activity demethylase activity molecular function activator activity molecular function regulator activity transcription regulator activator activity RNA binding binding nucleic acid binding single-stranded RNA binding oxidoreductase activity molecular transducer activity signaling receptor activity protein demethylase activity catalytic activity, acting on a protein catalytic activity demethylase activity molecular function activator activity molecular function regulator activity transcription regulator activator activity RNA binding binding nucleic acid binding single-stranded RNA binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid oxidative RNA demethylase activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity peptidyl-lysine 5-dioxygenase activity histone demethylase activity histone H3R2 demethylase activity histone H3 demethylase activity histone modifying activity histone H4 demethylase activity histone H4R3 demethylase activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding protein-containing complex binding P-TEFb complex binding identical protein binding protein binding	developmental process cellular developmental process cell differentiation cellular process import into cell localization transport phagocytosis endocytosis establishment of localization RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression developmental process cellular developmental process cell differentiation cellular process import into cell localization transport phagocytosis endocytosis establishment of localization RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process mRNA processing mRNA metabolic process RNA processing oxidative RNA demethylation RNA modification oxidative demethylation macromolecule modification demethylation multicellular organismal process blood vessel morphogenesis tube development angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development animal gross anatomical part developmental process blood vessel development system development RNA splicing regulation of cellular process regulation of mRNA splicing, via spliceosome regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of RNA splicing regulation of gene expression RNA splicing, via transesterification reactions mRNA splicing, via spliceosome regulation of macromolecule biosynthetic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process regulation of metabolic process peptidyl-lysine modification peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine peptidyl-lysine hydroxylation protein hydroxylation protein metabolic process protein modification process regulation of cellular component organization negative regulation of biological process negative regulation of protein homooligomerization regulation of protein oligomerization cellular component organization cellular component biogenesis regulation of protein homooligomerization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly negative regulation of cellular process protein homooligomerization cellular component organization or biogenesis negative regulation of protein oligomerization negative regulation of cellular component organization protein-containing complex organization regulation of cellular component biogenesis negative regulation of protein-containing complex assembly protein complex oligomerization 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 regulation of RNA biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II organelle organization organelle assembly membraneless organelle assembly chromatin organization chromatin remodeling	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 cytoplasm cytosol cell periphery plasma membrane membrane nucleoplasm protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050910	JMJD6 family arginine demethylases/lysyl-hydroxylases	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003347	JmjC domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	: Q6NYC1	acute myeloid leukemia large cell medulloblastoma malignant glioma ovarian cancer atypical teratoid rhabdoid tumor lung cancer medulloblastoma psoriasis glioblastoma malignant ependymoma osteosarcoma Sjogren syndrome

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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.