8JNR | pdb_00008jnr

Crystal structure of human ALKBH3 bound to 3mC containing ssDNA through distal crosslink

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Clavaminate synthase-like	8042867	3001848	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Clavaminate synthase-like	8042867	3001848	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Clavaminate synthase-like	8042867	3001848	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Clavaminate synthase-like	8042867	3001848	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
K, L, M, N	Light Chain	IGKV1	Kappa	alpha-ketoglutarate-dependent dioxygenase alkb homolog 3	SAbDab (2025-11-28)
G, H, I, J	Heavy Chain	IGHV3	-	alpha-ketoglutarate-dependent dioxygenase alkb homolog 3	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, D, E	PF13532	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy_2)	2OG-Fe(II) oxygenase superfamily		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
K, L, M, N	Synthetic antibody light chain	-	-	-
G, H, I, J	Synthetic antibody heavy chain	-	-	-
B, F	DNA	-	-	-
A, C, D, E	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3	cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding DNA demethylase activity broad specificity oxidative DNA demethylase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding DNA demethylase activity broad specificity oxidative DNA demethylase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 2-oxoglutarate-dependent dioxygenase activity catalytic activity demethylase activity dioxygenase activity catalytic activity, acting on RNA oxidative RNA demethylase activity organic acid binding carbohydrate binding vitamin binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding mRNA N1-methyladenosine dioxygenase activity	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process translation gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of cytoplasmic translation negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process cytoplasmic translation metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of cytoplasmic translation regulation of metabolic process cellular response to stimulus response to stimulus DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress DNA repair cell population proliferation DNA alkylation repair	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, D, E	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A, C, D, E	IPR037151	Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily	Homologous Superfamily
A, C, D, E	IPR027450	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	Domain
A, C, D, E	IPR032854	Alkylated DNA repair protein alkB homologue 3	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, D, E	Pharos: Q96Q83	attention deficit hyperactivity disorder, inattentive type medulloblastoma osteosarcoma

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.