6YW4

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a RaPID-derived silent allosteric cyclic peptide 3C (14-mer)

External Resource: Annotation

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

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_3	e6yw4A1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: 2OG-FeII_Oxy_3	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13640	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy_3)	2OG-Fe(II) oxygenase superfamily	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER)	-	-	-
A	Egl nine homolog 1	cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding peptidyl-proline 4-dioxygenase activity oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen peptidyl-proline dioxygenase activity catalytic activity cation binding transition metal ion binding iron ion binding ion binding binding ferrous iron binding metal ion binding small molecule binding peptidyl-proline 4-dioxygenase activity oxidoreductase activity catalytic activity, acting on a protein oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen peptidyl-proline dioxygenase activity catalytic activity 2-oxoglutarate-dependent 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 hypoxia-inducible factor-proline dioxygenase activity protein binding enzyme binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis regulation of angiogenesis anatomical structure development anatomical structure formation involved in morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development heart development cardiac chamber morphogenesis animal organ development heart morphogenesis ventricular septum development cardiac septum development cardiac septum morphogenesis ventricular septum morphogenesis cardiac chamber development animal organ morphogenesis cardiac ventricle development regulation of cellular process negative regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process negative regulation of molecular function primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity metabolic process cellular process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cardiac muscle tissue development tissue development muscle tissue morphogenesis striated muscle tissue development muscle structure development tissue morphogenesis cardiac muscle tissue morphogenesis muscle organ development muscle tissue development muscle organ morphogenesis placenta development chordate embryonic development labyrinthine layer development embryo development in utero embryonic development embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus regulation protein catabolic process at synapse catabolic process regulation of catabolic process regulation protein catabolic process at postsynapse negative regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity negative regulation of cyclic-nucleotide phosphodiesterase activity negative regulation of catalytic activity regulation of cyclic-nucleotide phosphodiesterase activity heart trabecula formation heart trabecula morphogenesis trabecula formation trabecula morphogenesis intracellular oxygen homeostasis positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of cellular component organization regulation of modification of synaptic structure cellular component organization regulation of synapse organization cell junction organization regulation of synapse structure or activity regulation of modification of postsynaptic structure synapse organization cellular component organization or biogenesis regulation of biological quality modification of synaptic structure modification of postsynaptic structure response to nitric oxide response to oxygen-containing compound response to nitrogen compound	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle synapse cell junction glutamatergic synapse postsynaptic density postsynapse neuron to neuron synapse cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle synapse cell junction glutamatergic synapse postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A	IPR002893	Zinc finger, MYND-type	Domain
A	IPR044862	Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain	Domain
A	IPR051559	Hypoxia-inducible factor prolyl hydroxylases	Family
A	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9GZT9	erythrocytosis, familial, 3 familial polycythemia polycythemia ovarian cancer Refractory anemia (clinical) toxic encephalopathy acquired polycythemia vera facioscapulohumeral muscular dystrophy glioblastoma malignant glioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma adrenal medulla cancer atypical teratoid rhabdoid tumor large cell medulloblastoma erythrocytosis, familial, 3 familial polycythemia polycythemia ovarian cancer Refractory anemia (clinical) toxic encephalopathy acquired polycythemia vera facioscapulohumeral muscular dystrophy glioblastoma malignant glioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma adrenal medulla cancer atypical teratoid rhabdoid tumor large cell medulloblastoma osteosarcoma secondary polycythemia benign neoplasm of adrenal gland erythropoietin polycythemia lung cancer myopathy

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.