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- PDB-1yci: Factor inhibiting HIF-1 alpha in complex with N-(carboxycarbonyl)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yci | ||||||
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Title | Factor inhibiting HIF-1 alpha in complex with N-(carboxycarbonyl)-D-phenylalanine | ||||||
![]() | Hypoxia-inducible factor 1 alpha inhibitor | ||||||
![]() | Transcription regulator / oxidoreductase / FIH / HIF / DSBH / OXYGENASE / TRANSCRIPTION / HYPOXIA / INHIBITOR 2-OXOGLUTARATE / ASPARAGINYL HYDROXYLASE / HYDROXYLASE N-(CARBOXYCARBONYL)-D-PHENYLALANINE / NOFD / NDF | ||||||
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 | ![]() ![]() | ||||||
![]() | McDonough, M.A. / Schofield, C.J. | ||||||
![]() | ![]() Title: Selective inhibition of factor inhibiting hypoxia-inducible factor Authors: McDonough, M.A. / McNeill, L.A. / Tilliet, M. / Papamicael, C.A. / Chen, Q.Y. / Banerji, B. / Hewitson, K.S. / Schofield, C.J. #1: ![]() Title: Structure of factor-inhibiting hypoxia-inducible factor (HIF) reveals mechanism of oxidative modification of HIF-1 alpha Authors: Elkins, J.M. / Hewitson, K.S. / McNeill, L.A. / Seibel, J.F. / Schlemminger, I. / 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 | ![]() | 85.6 KB | Display | ![]() |
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PDB format | ![]() | 63.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.6 KB | Display | ![]() |
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Full document | ![]() | 462.4 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h2nS 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
#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 | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63 % Description: Rejection criteria as rejection probability, REJECTION CRITERIA (PROBABILITY)) : 0.0001 |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.2M AMMONIUM SULPHATE, 4% PEG400, 0.1M HEPES PH7.5 ARGON ATMOSPHERE, 28MG/ML PROTEIN WITH 1MM FE(II), 10MM N-(CARBOXYCARBONYL)-D-PHENYLALANINE, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2004 |
Radiation | Monochromator: double crystal Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→43.45 Å / Num. all: 16510 / Num. obs: 16510 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1619 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS WITH 1H2N Starting model: 1H2N Resolution: 2.7→43.45 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.9107 Å2 / ksol: 0.352278 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→43.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
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Xplor file |
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