3H8X

Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2B Superfamily	Clavaminate synthase-like	8088228	3001848	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	2OG-FeII_Oxy_2	e3h8xA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.590	Mainly Beta	Sandwich	Jelly Rolls	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2	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 cytosine C-5 DNA demethylase activity hydrolase activity DNA binding sequence-specific DNA 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 cytosine C-5 DNA demethylase activity hydrolase activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding rDNA binding cation binding transition metal ion binding iron ion binding ion binding ferrous iron binding metal ion binding small molecule binding	oxidative demethylation demethylation metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA modification organic substance metabolic process DNA demethylation DNA dealkylation macromolecule modification macromolecule metabolic process oxidative demethylation demethylation metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA modification organic substance metabolic process DNA demethylation DNA dealkylation macromolecule modification macromolecule metabolic process cellular response to stimulus response to stimulus DNA alkylation repair cellular response to stress DNA damage response response to stress cellular process DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nucleoplasm
B	5'-D(CPTPGPTP(ME6)PTP(2YR)PAPTPTPGPCP*G)-3'	-	-	-
C	5'-D(TPCPGPCPAPAPTPAPAPGPAPCP*A)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR032852	DNA oxidative demethylase ALKBH2	Family
A	IPR037151	Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily	Homologous Superfamily
A	IPR027450	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	Domain
A	IPR005123	Oxoglutarate/iron-dependent dioxygenase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q6NS38	medulloblastoma ovarian cancer

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.