6IMC

Crystal Structure of ALKBH1 in complex with Mn(II) and N-Oxalylglycine

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF13532	e6imcA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PF13532	ECOD (1.6)
B	PF13532	e6imcB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PF13532	ECOD (1.6)
C	PF13532	e6imcC1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PF13532	ECOD (1.6)
D	PF13532	e6imcD1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PF13532	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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
A, B, C, D	Nucleic acid dioxygenase ALKBH1	cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding tRNA demethylase 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 catalytic activity, acting on a tRNA demethylase activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding tRNA demethylase 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 catalytic activity, acting on a tRNA demethylase activity dioxygenase activity oxidoreductase activity oxidative RNA demethylase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity RNA binding organic cyclic compound binding tRNA binding nucleic acid binding protein binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity chemoattractant activity signaling receptor activator activity DNA-(apurinic or apyrimidinic site) endonuclease activity catalytic activity, acting on DNA class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity carbon-oxygen lyase activity DNA demethylase activity broad specificity oxidative DNA demethylase activity DNA N6-methyladenine demethylase activity	developmental process cellular developmental process cell differentiation cellular process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process tRNA wobble cytosine modification tRNA wobble base modification RNA processing cellular metabolic process developmental process cellular developmental process cell differentiation cellular process cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process tRNA wobble cytosine modification tRNA wobble base modification RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process macromolecule modification nucleic acid catabolic process metabolic process macromolecule metabolic process placenta development animal organ development anatomical structure development regulation of cellular process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translational elongation protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process translation regulation of cellular biosynthetic process regulation of gene expression regulation of translation translational elongation regulation of macromolecule biosynthetic process regulation of metabolic process cellular response to stimulus response to stimulus DNA metabolic process DNA alkylation repair cellular response to stress DNA damage response response to stress DNA repair developmental growth growth oxidative RNA demethylation oxidative demethylation demethylation neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development mitochondrial translation regulation of mitochondrial gene expression mitochondrial gene expression regulation of mitochondrial translation RNA repair translational initiation regulation of translational initiation neuron migration nervous system development generation of neurons neurogenesis cell migration cell motility system development positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic protein-DNA complex organization cellular component organization positive regulation of metabolic process positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process protein-containing complex organization epigenetic regulation of gene expression positive regulation of gene expression positive regulation of cellular biosynthetic process regulation of translational initiation by tRNA modification plasma membrane bounded cell projection organization cell projection organization cell development neuron projection development neuron differentiation neuron development	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex protein-DNA complex euchromatin chromatin chromosome intracellular non-membrane-bounded organelle non-membrane-bounded organelle endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004574	Alkylated DNA repair protein AlkB	Family
A, B, C, D	IPR027450	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	Domain
A, B, C, D	IPR005123	Oxoglutarate/iron-dependent dioxygenase	Domain
A, B, C, D	IPR037151	Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily	Homologous Superfamily

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 R01GM133198.