4QKD | pdb_00004qkd

Crystal structure of human ALKBH7 in complex with alpha-ketoglutarate and Mn(II)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	e4qkdA1	A: RuvA-C	X: post-HMGL domain-like	H: post-HMGL domain-like	T: Acetyltransf_9	F:	ECOD (20:10:01)
C	e4qkdC1	A: RuvA-C	X: post-HMGL domain-like	H: post-HMGL domain-like	T: Acetyltransf_9	F:	ECOD (20:10:01)
B	e4qkdB1	A: RuvA-C	X: post-HMGL domain-like	H: post-HMGL domain-like	T: Acetyltransf_9	F:	ECOD (20:10:01)

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)
C	2.60.120.590	Mainly Beta	Sandwich	Jelly Rolls	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	CATH (4.3.0)
B	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, B, C	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	Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial	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 cation binding ion binding 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 cation binding ion binding binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process lipid metabolic process biological regulation programmed necrotic cell death regulation of membrane permeability regulation of biological quality cell death regulation of mitochondrial membrane permeability programmed cell death regulation of mitochondrial membrane permeability involved in programmed necrotic cell death regulation of biological process regulation of cellular process regulation of lipid storage lipid storage nutrient storage RNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process oxidative RNA demethylation RNA modification oxidative demethylation macromolecule modification demethylation macromolecule metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR032870	Alpha-ketoglutarate-dependent dioxygenase alkB homologue 7-like	Family
A, B, C	IPR037151	Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily	Homologous Superfamily
A, B, C	IPR027450	Alpha-ketoglutarate-dependent dioxygenase AlkB-like	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q9BT30	diabetes mellitus pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia medulloblastoma pancreatic intraductal papillary-mucinous carcinoma ulcerative colitis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C	LED	Parent Component: LEU RESID: AA0444 PSI-MOD : (2S,4R)-5-oxoleucine MOD:01374

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.

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