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- PDB-2yc0: FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2-HYDROXYGLUTARATE -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yc0 | ||||||
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Title | FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2-HYDROXYGLUTARATE | ||||||
![]() | HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR | ||||||
![]() | OXIDOREDUCTASE / DIOXYGENASE / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / ASPARAGINYL/ASPARTYL HYDROXYLASE / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / ANKYRIN REPEAT DOMAIN / ARD / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / S-NITROSYLATION | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Chowdhury, R. / Clifton, I.J. / Schofield, C.J. | ||||||
![]() | ![]() Title: The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. Authors: Chowdhury, R. / Yeoh, K.K. / Tian, Y.M. / Hillringhaus, L. / Bagg, E.A. / Rose, N.R. / Leung, I.K. / Li, X.S. / Woon, E.C. / Yang, M. / McDonough, M.A. / King, O.N. / Clifton, I.J. / Klose, ...Authors: Chowdhury, R. / Yeoh, K.K. / Tian, Y.M. / Hillringhaus, L. / Bagg, E.A. / Rose, N.R. / Leung, I.K. / Li, X.S. / Woon, E.C. / Yang, M. / McDonough, M.A. / King, O.N. / Clifton, I.J. / Klose, R.J. / Claridge, T.D. / Ratcliffe, P.J. / Schofield, C.J. / Kawamura, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.1 KB | Display | ![]() |
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PDB format | ![]() | 65 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.9 KB | Display | ![]() |
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Full document | ![]() | 478.2 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ybkC ![]() 2ybpC ![]() 2ybsC ![]() 2ydeC ![]() 1h2kS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40610.551 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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-Non-polymers , 5 types, 102 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/2HG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/2HG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / | ||||
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#3: Chemical | ChemComp-2HG / ( | ||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES PH7.5, 1.6M AMMONIUM SULFATE, 6% PEG400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→42.84 Å / Num. obs: 29618 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.15→2.25 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.7 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H2K Resolution: 2.15→42.84 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 216130.37 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.2205 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→42.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 8
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Xplor file |
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