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Yorodumi- PDB-7a1p: FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II), 4-propyl-2-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a1p | ||||||
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Title | FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH ZN(II), 4-propyl-2-oxoglutarate, AND CONSENSUS ANKYRIN REPEAT DOMAIN (20-MER) | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Hypoxia-inducible factor asparagine hydroxylase / Dioxygenase | ||||||
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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Nakashima, Y. / Brewitz, L. / Schofield, C.J. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: 2-Oxoglutarate derivatives can selectively enhance or inhibit the activity of human oxygenases. Authors: Nakashima, Y. / Brewitz, L. / Tumber, A. / Salah, E. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a1p.cif.gz | 278.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a1p.ent.gz | 189.6 KB | Display | PDB format |
PDBx/mmJSON format | 7a1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a1p_validation.pdf.gz | 608.9 KB | Display | wwPDB validaton report |
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Full document | 7a1p_full_validation.pdf.gz | 610.8 KB | Display | |
Data in XML | 7a1p_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 7a1p_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/7a1p ftp://data.pdbj.org/pub/pdb/validation_reports/a1/7a1p | HTTPS FTP |
-Related structure data
Related structure data | 7a1jC 7a1kC 7a1lC 7a1mC 7a1nC 7a1oC 7a1qC 7a1sC 1h2kS S: Starting model for refinement C: citing same article (ref.) |
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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 / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 40328.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1AN, FIH1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one ...References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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#2: Protein/peptide | Mass: 2165.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 240 molecules
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | ChemComp-QW2 / ( | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6M AMMONIUM SULPHATE, 6% PEG 400, 0.1M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.759→74.275 Å / Num. obs: 104634 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 40.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.759→1.79 Å / Redundancy: 28 % / Rmerge(I) obs: 6.504 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2745 / CC1/2: 0.365 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H2K Resolution: 1.76→56.2 Å / SU ML: 0.2743 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.3147 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→56.2 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 22.1749426385 Å / Origin y: -27.5129790581 Å / Origin z: 8.57020973402 Å
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Refinement TLS group | Selection details: all |