6YVT

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d6yvta_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	proly-4-hydroxylase (P4H, PHD) like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6yvtb_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	proly-4-hydroxylase (P4H, PHD) like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6yvtc_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	proly-4-hydroxylase (P4H, PHD) like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6yvtd_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	proly-4-hydroxylase (P4H, PHD) like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6yvtf_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	proly-4-hydroxylase (P4H, PHD) like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6yvte_	All beta proteins	Double-stranded beta-helix	Clavaminate synthase-like	proly-4-hydroxylase (P4H, PHD) like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

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	e6yvtA1	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)
B	2OG-FeII_Oxy_3	e6yvtB1	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)
C	2OG-FeII_Oxy_3	e6yvtC1	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)
D	2OG-FeII_Oxy_3	e6yvtD1	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)
F	2OG-FeII_Oxy_3	e6yvtF1	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)
E	2OG-FeII_Oxy_3	e6yvtE1	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)

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 (utative)
B	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
C	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
D	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
F	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
E	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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
A, B, C, D, E A, B, C, D, E, F	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 cellular biosynthetic 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 cellular metabolic process negative regulation of molecular function primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity metabolic process regulation of macromolecule biosynthetic process cellular 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 cellular metabolic 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 positive regulation of cellular 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle synapse cell junction glutamatergic synapse postsynaptic density postsynapse neuron to neuron synapse intracellular anatomical structure cytoplasm cellular anatomical entity 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, B, C, D, E A, B, C, D, E, F	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002893	Zinc finger, MYND-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044862	Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR051559	Hypoxia-inducible factor prolyl hydroxylases	Family
A, B, C, D, E A, B, C, D, E, F	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	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 R01GM133198.