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Yorodumi- PDB-2hbu: Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hbu | ||||||
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Title | Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor | ||||||
Components | Egl nine homolog 1 | ||||||
Keywords | OXIDOREDUCTASE / HIF / prolyl hydroxylase / EGLN / 2-oxoglutarate / hypoxia inducible factor | ||||||
Function / homology | Function and homology information hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity / cardiac muscle tissue morphogenesis ...hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity / cardiac muscle tissue morphogenesis / heart trabecula formation / regulation of modification of postsynaptic structure / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / negative regulation of DNA-binding transcription factor activity / cellular response to hypoxia / intracellular iron ion homeostasis / postsynaptic density / response to hypoxia / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Evdokimov, A.G. / Walter, R.L. / Mekel, M. / Pokross, M.E. / Kawamoto, R. / Boyer, A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of HIF prolyl hydroxylase in complex with a biologically active inhibitor Authors: Evdokimov, A.G. / Walter, R.L. / Mekel, M. / Pokross, M.E. / Kawamoto, R. / Boyer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hbu.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hbu.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/2hbu ftp://data.pdbj.org/pub/pdb/validation_reports/hb/2hbu | HTTPS FTP |
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-Related structure data
Related structure data | 2hbtSC 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
#1: Protein | Mass: 27832.674 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1 / Plasmid: pET45-DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)* References: UniProt: Q9GZT9, 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: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-UN9 / |
#4: 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: 2.57 Å3/Da / Density % sol: 52.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 200-300 mM (NH4)2SO4, 100 mM NaOAc pH 4.8-5.4, 22-25% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 8, 2005 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 24248 / Num. obs: 24248 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.95 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HBT Resolution: 1.85→32.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.815 / SU ML: 0.082 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.709 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→32.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.851→1.899 Å / Total num. of bins used: 20
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