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- PDB-5l9b: HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH 2-OXOGLUTA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l9b | ||||||
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Title | HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-1ALPHA CODD (556-574) | ||||||
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![]() | OXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN1 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / CYTOPLASM / TRANSCRIPTION/EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / UBL CONJUGATION / POLYMORPHISM / VITAMIN C / ZINC-FINGER / FAMILIAL ERYTHROCYTOSIS / BREAST CANCER / TRANSCRIPTION COMPLEX | ||||||
Function / homology | ![]() epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / regulation of transforming growth factor beta2 production / peptidyl-proline dioxygenase activity / connective tissue replacement involved in inflammatory response wound healing / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / cardiac ventricle morphogenesis / negative regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / regulation protein catabolic process at postsynapse / positive regulation of mitophagy / retina vasculature development in camera-type eye / Cellular response to hypoxia / intestinal epithelial cell maturation / negative regulation of growth / regulation of protein neddylation / collagen metabolic process / PTK6 Expression / intracellular oxygen homeostasis / negative regulation of bone mineralization / B-1 B cell homeostasis / vascular endothelial growth factor production / labyrinthine layer development / cardiac muscle tissue morphogenesis / 2-oxoglutarate-dependent dioxygenase activity / transcription regulator activator activity / dopaminergic neuron differentiation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / heart trabecula formation / regulation of modification of postsynaptic structure / lactate metabolic process / STAT3 nuclear events downstream of ALK signaling / positive regulation of cytokine production involved in inflammatory response / negative regulation of thymocyte apoptotic process / L-ascorbic acid binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / motile cilium / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / negative regulation of TOR signaling / response to iron ion / response to muscle activity / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / embryonic hemopoiesis / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / PTK6 promotes HIF1A stabilization / regulation of aerobic respiration / digestive tract morphogenesis / response to nitric oxide / muscle cell cellular homeostasis / ventricular septum morphogenesis / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / positive regulation of epithelial cell migration / bone mineralization / heart looping / outflow tract morphogenesis / E-box binding / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of vascular endothelial growth factor production / TOR signaling / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / embryonic placenta development / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / cellular response to interleukin-1 / regulation of angiogenesis / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / positive regulation of chemokine production / axon cytoplasm / positive regulation of endothelial cell proliferation / lactation / positive regulation of glycolytic process / negative regulation of miRNA transcription / positive regulation of erythrocyte differentiation / positive regulation of nitric-oxide synthase activity / response to reactive oxygen species / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / euchromatin / visual learning / ferrous iron binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chowdhury, R. / Schofield, C.J. | ||||||
![]() | ![]() Title: Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases. Authors: Chowdhury, R. / Leung, I.K. / Tian, Y.M. / Abboud, M.I. / Ge, W. / Domene, C. / Cantrelle, F.X. / Landrieu, I. / Hardy, A.P. / Pugh, C.W. / Ratcliffe, P.J. / Claridge, T.D. / Schofield, C.J. #1: ![]() Title: Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases. Authors: Chowdhury, R. / McDonough, M.A. / Mecinovic, J. / Loenarz, C. / Flashman, E. / Hewitson, K.S. / Domene, C. / Schofield, C.J. #2: ![]() Title: Selective small molecule probes for the hypoxia inducible factor (HIF) prolyl hydroxylases. Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / ...Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / Kawamura, A. / Lee, M.K. / van Eeden, F. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.6 KB | Display | ![]() |
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PDB format | ![]() | 86.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
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Full document | ![]() | 457.1 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l9rC ![]() 5l9vC ![]() 5la9C ![]() 5lasC ![]() 5latC ![]() 5lb6C ![]() 5lbbC ![]() 5lbcC ![]() 5lbeC ![]() 5lbfC ![]() 3hqrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27978.762 Da / Num. of mol.: 2 / Fragment: UNP residues 181-426 / Mutation: C201A, R398A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase #2: Protein/peptide | Mass: 2254.532 Da / Num. of mol.: 2 / Fragment: UNP residues 556-574 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2016 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.438 |
Reflection | Resolution: 1.95→40.193 Å / Num. obs: 31425 / % possible obs: 99.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 20.51 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 8.6543 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.713 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HQR Resolution: 1.95→40.193 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.48 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.788 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→40.193 Å
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Refine LS restraints |
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LS refinement shell |
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