2A1X

Human phytanoyl-coa 2-hydroxylase in complex with iron and 2-oxoglutarate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2a1xa1	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	PhyH-like	Phytanoyl-CoA dioxygenase, PhyH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PhyH-like	8024096	4002133	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Clavaminate synthase-like	8036475	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)
A	PhyH_1	e2a1xA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05721	Phytanoyl-CoA dioxygenase (PhyH) (PhyH)	Phytanoyl-CoA dioxygenase (PhyH)	This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficie ...	This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Phytanoyl-CoA dioxygenase	cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity phytanoyl-CoA dioxygenase activity dioxygenase activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity phytanoyl-CoA dioxygenase activity dioxygenase activity organic acid binding carbohydrate binding vitamin binding organic cyclic compound binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding	cellular metabolic process cellular lipid metabolic process primary metabolic process metabolic process cellular process isoprenoid metabolic process lipid metabolic process catabolic process oxoacid metabolic process organic acid catabolic process organic acid metabolic process cellular lipid catabolic process cellular catabolic process monocarboxylic acid catabolic process cellular metabolic process cellular lipid metabolic process primary metabolic process metabolic process cellular process isoprenoid metabolic process lipid metabolic process catabolic process oxoacid metabolic process organic acid catabolic process organic acid metabolic process cellular lipid catabolic process cellular catabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process small molecule metabolic process lipid oxidation fatty acid metabolic process lipid catabolic process carboxylic acid metabolic process lipid modification fatty acid catabolic process fatty acid alpha-oxidation monocarboxylic acid metabolic process small molecule catabolic process 2-oxoglutarate metabolic process dicarboxylic acid metabolic process 2-oxobutyrate metabolic process short-chain fatty acid metabolic process short-chain fatty acid catabolic process 2-oxobutyrate catabolic process methyl-branched fatty acid metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle peroxisome microbody cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen non-motile cilium cell projection 9+0 non-motile cilium cilium plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR047128	Phytanoyl-CoA dioxygenase	Family
A	IPR008775	Phytanoyl-CoA dioxygenase-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O14832	adult Refsum disease peroxisomal disease retinitis pigmentosa Charcot-Marie-Tooth disease inborn errors of metabolism oligodendroglioma psoriasis Refsum Disease, Phytanoyl-CoA Hydroxylase Deficiency spina bifida astrocytic tumor cone-rod dystrophy large cell medulloblastoma ovarian cancer retinal degeneration ulcerative colitis adult Refsum disease peroxisomal disease retinitis pigmentosa Charcot-Marie-Tooth disease inborn errors of metabolism oligodendroglioma psoriasis Refsum Disease, Phytanoyl-CoA Hydroxylase Deficiency spina bifida astrocytic tumor cone-rod dystrophy large cell medulloblastoma ovarian cancer retinal degeneration ulcerative colitis cataract ductal breast carcinoma in situ malignant mesothelioma

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.