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Yorodumi- PDB-5f0a: CRYSTAL STRUCTURE OF PVX_084705 WITH BOUND 1-tert-butyl-3-(3-chlo... -
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-Basic information
Entry | Database: PDB / ID: 5f0a | |||||||||
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Title | CRYSTAL STRUCTURE OF PVX_084705 WITH BOUND 1-tert-butyl-3-(3-chlorophenoxy)-1H-pyrazolo[3,4-d]pyrimidin-4-amine INHIBITOR | |||||||||
Components | cGMP-dependent protein kinase, putative | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / KINASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / cGMP binding / phosphorylation / endoplasmic reticulum membrane / signal transduction / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | |||||||||
Authors | Walker, J.R. / Wernimont, A.K. / He, H. / Seitova, A. / Loppnau, P. / Sibley, L.D. / Graslund, S. / Hutchinson, A. / Bountra, C. / Weigelt, J. ...Walker, J.R. / Wernimont, A.K. / He, H. / Seitova, A. / Loppnau, P. / Sibley, L.D. / Graslund, S. / Hutchinson, A. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / El Bakkouri, M. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: To be published Title: CRYSTAL STRUCTURE OF PVX_084705 WITH BOUND INHIBITOR Authors: Walker, J.R. / Wernimont, A.K. / He, H. / Seitova, A. / Loppnau, P. / Sibley, L.D. / Graslund, S. / Hutchinson, A. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / ...Authors: Walker, J.R. / Wernimont, A.K. / He, H. / Seitova, A. / Loppnau, P. / Sibley, L.D. / Graslund, S. / Hutchinson, A. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / El Bakkouri, M. / Structural Genomics Consortium (SGC) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f0a.cif.gz | 334.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f0a.ent.gz | 273.4 KB | Display | PDB format |
PDBx/mmJSON format | 5f0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f0a_validation.pdf.gz | 715.3 KB | Display | wwPDB validaton report |
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Full document | 5f0a_full_validation.pdf.gz | 717.5 KB | Display | |
Data in XML | 5f0a_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 5f0a_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f0a ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f0a | HTTPS FTP |
-Related structure data
Related structure data | 4myi 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
#1: Protein | Mass: 96726.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote) Strain: Salvador I / Gene: PVX_084705 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: A5K0N4 |
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#2: Chemical | ChemComp-1FB / |
#3: 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: 3.94 Å3/Da / Density % sol: 68.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5% TACSIMATE, 0.1 M HEPES PH 7.0, 10% PEG 5000 MME, 16% SPERMIDINE PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97945 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 45908 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.842 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4MYI 4myi Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 23.814 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.258 / 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: 71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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