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Open data
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Basic information
Entry | Database: PDB / ID: 5opc | ||||||
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Title | Factor Inhibiting HIF (FIH) in complex with zinc and Vadadustat | ||||||
![]() | Hypoxia-inducible factor 1-alpha inhibitor | ||||||
![]() | OXIDOREDUCTASE / ON-HEME / DIOXYGENASE / OXYGENASE / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / ASPARAGINYL/ASPARTYL HYDROXYLASE / EPIGENETIC REGULATION / SIGNALING / ARD / BETA-HYDROXYLATION / ACTIVATOR-INHIBITOR / OXIDOREDUCTASE-PEPTIDE COMPLEX | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Leissing, T.M. / Schofield, C.J. / Clifton, I.J. / Lu, X. / Zhang, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular and cellular mechanisms of HIF prolyl hydroxylase inhibitors in clinical trials. Authors: Yeh, T.L. / Leissing, T.M. / Abboud, M.I. / Thinnes, C.C. / Atasoylu, O. / Holt-Martyn, J.P. / Zhang, D. / Tumber, A. / Lippl, K. / Lohans, C.T. / Leung, I.K.H. / Morcrette, H. / Clifton, I. ...Authors: Yeh, T.L. / Leissing, T.M. / Abboud, M.I. / Thinnes, C.C. / Atasoylu, O. / Holt-Martyn, J.P. / Zhang, D. / Tumber, A. / Lippl, K. / Lohans, C.T. / Leung, I.K.H. / Morcrette, H. / Clifton, I.J. / Claridge, T.D.W. / Kawamura, A. / Flashman, E. / Lu, X. / Ratcliffe, P.J. / Chowdhury, R. / Pugh, C.W. / 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 | ![]() | 211.8 KB | Display | ![]() |
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PDB format | ![]() | 172.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5op6C ![]() 5op8C ![]() 5ox5C ![]() 5ox6C ![]() 1h2kS S: Starting model for refinement C: citing same article ( |
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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: 40415.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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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-Non-polymers , 5 types, 84 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/A1Z.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/A1Z.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-A1Z / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.7 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH7.5, 1.7M ammonium sulfate, 5.5% PEG 400 Temp details: ambient |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo cooling |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→86.8 Å / Num. obs: 26216 / % possible obs: 100 % / Redundancy: 17.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.036 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 17.5 % / Rmerge(I) obs: 1.78 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3748 / CC1/2: 0.689 / Rpim(I) all: 0.435 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1h2k Resolution: 2.3→75.067 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→75.067 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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