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Yorodumi- PDB-2yc0: FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2-HYDROXYGLUTARATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yc0 | ||||||
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Title | FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2-HYDROXYGLUTARATE | ||||||
Components | HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR | ||||||
Keywords | 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 | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Chowdhury, R. / Clifton, I.J. / Schofield, C.J. | ||||||
Citation | Journal: EMBO Rep. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yc0.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yc0.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 2yc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yc0_validation.pdf.gz | 472.9 KB | Display | wwPDB validaton report |
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Full document | 2yc0_full_validation.pdf.gz | 478.2 KB | Display | |
Data in XML | 2yc0_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 2yc0_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/2yc0 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/2yc0 | HTTPS FTP |
-Related structure data
Related structure data | 2ybkC 2ybpC 2ybsC 2ydeC 1h2kS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase |
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-Non-polymers , 5 types, 102 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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