3LDB | pdb_00003ldb

Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d3ldbc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Nothocricetulus migratorius ) [TaxId: 3122392 ],	SCOPe (2.08)
B	d3ldbb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Nothocricetulus migratorius ) [TaxId: 3122392 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Cytochrome_CBB3	e3ldbC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
B	Cytochrome_CBB3	e3ldbB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
A		e3ldbA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.120.650	Mainly Beta	Sandwich	Jelly Rolls	Cupin	CATH (4.3.0)
A	1.20.1280.270	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C	Antibody Fab Fragment	VH-CH1	Rattus norvegicus (Norway rat)	IGHV3-301, IGHJ201, IGHG2B*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2B_KAPPA	IMGT (202612-0)
B	Antibody Fab Fragment	L-KAPPA	Rattus norvegicus (Norway rat)	IGKV8S601, IGKJ2-301, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2B_KAPPA	IMGT (202612-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Heavy Chain	IGHV3	-	bifunctional arginine demethylase and lysyl-hydroxylasejmjd6	SAbDab (2026-03-27)
B	Light Chain	IGKV8	Kappa	bifunctional arginine demethylase and lysyl-hydroxylasejmjd6	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	antibody Fab fragment heavy chain	-	-	-
B	antibody Fab fragment light chain	-	-	-
A	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 heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development import into cell transport establishment of localization vesicle-mediated transport phagocytosis, recognition localization developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development import into cell transport establishment of localization vesicle-mediated transport phagocytosis, recognition localization phagocytosis cellular process cell recognition apoptotic cell clearance recognition of apoptotic cell endocytosis erythrocyte development cellular developmental process homeostatic process hemopoiesis cell development erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation immune system process cell differentiation myeloid cell development homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis sensory organ development eye development retina development in camera-type eye visual system development camera-type eye development sensory system development tube development respiratory tube development lung development respiratory system development RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process RNA processing oxidative RNA demethylation RNA modification oxidative demethylation macromolecule modification demethylation blood vessel morphogenesis angiogenesis sprouting angiogenesis vasculature development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development cell activation mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation T cell differentiation leukocyte differentiation 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 cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling signal transduction cell communication peptidyl-lysine modification peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine peptidyl-lysine hydroxylation peptidyl-amino acid modification 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 DNA-templated transcription 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 macrophage activation myeloid leukocyte activation kidney development renal system development 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	IPR050910	JMJD6 family arginine demethylases/lysyl-hydroxylases	Family
A	IPR003347	JmjC domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: 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

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.