3KHB | pdb_00003khb

Crystal structure of Escherichia coli AlkB with Co(II) and 2-OG

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3khbb_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	AlkB-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3khba_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	AlkB-like	automated matches	(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	SCOP2B Superfamily	Clavaminate synthase-like	8040788	3001848	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Clavaminate synthase-like	8040788	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)
B	COesterase, BD-FAE	e3khbB1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: COesterase, BD-FAE	ECOD (develop294)
A	Integrin_A_Ig_1	e3khbA1	A: alpha bundles	X: Profilin-like	H: sensor domains	T: sensor domains	F: Integrin_A_Ig_1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.590	Mainly Beta	Sandwich	Jelly Rolls	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	CATH (4.3.0)
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, B	Alpha-ketoglutarate-dependent dioxygenase alkB	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	oxidative demethylation demethylation metabolic process cellular process nucleobase-containing compound metabolic process RNA metabolic process primary metabolic process macromolecule metabolic process RNA repair nucleic acid metabolic process response to methyl methanesulfonate response to stimulus response to chemical response to oxygen-containing compound oxidative demethylation demethylation metabolic process cellular process nucleobase-containing compound metabolic process RNA metabolic process primary metabolic process macromolecule metabolic process RNA repair nucleic acid metabolic process 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 alkylation repair oxidative RNA demethylation RNA modification macromolecule modification	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

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.