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Open data
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Basic information
Entry | Database: PDB / ID: 2wa4 | ||||||
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Title | FACTOR INHIBITING HIF-1 ALPHA WITH N,3-dihydroxybenzamide | ||||||
![]() | HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR | ||||||
![]() | OXIDOREDUCTASE / HYDROXYLASE / DIOXYGENASE / TRANSCRIPTION / TRANSCRIPTION ACTIVATOR/INHIBITOR / HYPOXIA | ||||||
Function / homology | ![]() hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity / Notch binding / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Conejo-Garcia, A. / Lienard, B.M.R. / Clifton, I.J. / McDonough, M.A. / Schofield, C.J. | ||||||
![]() | ![]() Title: Structural basis for binding of cyclic 2-oxoglutarate analogues to factor-inhibiting hypoxia-inducible factor. Authors: Conejo-Garcia, A. / McDonough, M.A. / Loenarz, C. / McNeill, L.A. / Hewitson, K.S. / Ge, W. / Lienard, B.M. / Schofield, C.J. / Clifton, I.J. #1: ![]() Title: Structure of Factor-Inhibiting Hypoxia-Inducible Factor (Hif) Reveals Mechanism of Oxidative Modification of Hif-1Alpha Authors: Elkins, J. / Hewitson, K.S. / McNeill, L. / Seibel, J. / Schlemminger, I. / Pugh, C. / Ratcliffe, P. / 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 | ![]() | 154.5 KB | Display | ![]() |
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PDB format | ![]() | 124 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.6 KB | Display | ![]() |
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Full document | ![]() | 460.5 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w0xC ![]() 2wa3C ![]() 1h2nS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 40328.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase | ||||||
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#2: Chemical | ChemComp-FE2 / | ||||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Nonpolymer details | N,3-DIHYDROXYB | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 1.5M AMMONIUM SULFATE, 100MM HEPES PH 7.5, 3% PEG400, 1MM FESO4, 28MB/ML PROTEIN, 10MM SUBSTRATE. CRYSTALS ARE DEEP RED. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 10, 2004 / Details: RH COATED MIRROR |
Radiation | Monochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→37.77 Å / Num. obs: 20923 / % possible obs: 99 % / Redundancy: 9.1 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.49→2.62 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.8 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H2N Resolution: 2.5→75.38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 17.271 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED FROM TLS MODEL. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED FROM TLS MODEL. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.511 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→75.38 Å
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