2FDI

Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T (air 3 hours)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d2fdia_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	AlkB-like	Alkylated DNA repair protein AlkB	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2 Family	AlkB-like	8028409	4002139	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Clavaminate synthase-like	8040788	3001848	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth A]	2OG-FeII_Oxy_2	e2fdiA1	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)
B [auth A]	2.60.120.590	Mainly Beta	Sandwich	Jelly Rolls	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	5'-D(PTP(MA7)P*T)-3'	-	-	-
B [auth A]	Alkylated DNA repair protein alkB	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 cation binding transition metal ion binding iron ion binding ion 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 cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding catalytic activity, acting on RNA oxidative RNA demethylase activity	oxidative demethylation demethylation metabolic process cellular metabolic process RNA metabolic process cellular nitrogen compound metabolic process primary metabolic process RNA repair nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process heterocycle metabolic process nitrogen compound metabolic process oxidative demethylation demethylation metabolic process cellular metabolic process RNA metabolic process cellular nitrogen compound metabolic process primary metabolic process RNA repair nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process heterocycle metabolic process nitrogen compound metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process response to organic substance response to methyl methanesulfonate response to stimulus response to chemical response to oxygen-containing compound cellular response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair DNA modification DNA demethylation DNA dealkylation macromolecule modification DNA alkylation repair oxidative RNA demethylation RNA modification	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

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

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.