6YVT | pdb_00006yvt

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)
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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	RGM_N	e6yvtF1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: RGM_N	ECOD (develop294)
E	RGM_N	e6yvtE1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: RGM_N	ECOD (develop294)
D	RGM_N	e6yvtD1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: RGM_N	ECOD (develop294)
C	RGM_N	e6yvtC1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: RGM_N	ECOD (develop294)
B	RGM_N	e6yvtB1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: RGM_N	ECOD (develop294)
A	RGM_N	e6yvtA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: RGM_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
D	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)
B	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
A	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 enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity organic acid binding carbohydrate binding vitamin binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding hypoxia-inducible factor-proline dioxygenase activity zinc ion binding 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 anatomical structure morphogenesis multicellular organism development tube morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis anatomical structure development 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 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 cellular process regulation protein catabolic process at synapse catabolic process regulation of cellular process metabolic process regulation of catabolic process regulation of metabolic process regulation protein catabolic process at postsynapse neuron apoptotic process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process heart trabecula formation heart trabecula morphogenesis trabecula formation trabecula morphogenesis intracellular oxygen homeostasis regulation of cellular response to hypoxia signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of cellular response to stress regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication negative regulation of hypoxia-inducible factor-1alpha signaling pathway regulation of intracellular signal transduction regulation of response to stress hypoxia-inducible factor-1alpha signaling pathway negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction negative regulation of cellular response to hypoxia regulation of response to stimulus regulation of hypoxia-inducible factor-1alpha signaling pathway regulation of cell communication positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription 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 synapse cell junction glutamatergic synapse postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization organelle asymmetric synapse membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization organelle asymmetric synapse membrane-bounded organelle intracellular organelle nucleus intracellular membrane-bounded organelle

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.