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Yorodumi- PDB-7q4a: Toxoplasma gondii PRP4K kinase domain (L715F) bound to altiratinib -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q4a | |||||||||
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Title | Toxoplasma gondii PRP4K kinase domain (L715F) bound to altiratinib | |||||||||
Components | Non-specific serine/threonine protein kinase | |||||||||
Keywords | SPLICING / Spliceosome / kinase inhibitor / splicing inhibition | |||||||||
Function / homology | Function and homology information mRNA cis splicing, via spliceosome / protein serine/threonine/tyrosine kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding Similarity search - Function | |||||||||
Biological species | Toxoplasma gondii (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | |||||||||
Authors | Swale, C. / Bellini, V. / Bowler, M. | |||||||||
Funding support | France, 2items
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Citation | Journal: Sci Transl Med / Year: 2022 Title: Altiratinib blocks Toxoplasma gondii and Plasmodium falciparum development by selectively targeting a spliceosome kinase. Authors: Swale, C. / Bellini, V. / Bowler, M.W. / Flore, N. / Brenier-Pinchart, M.P. / Cannella, D. / Belmudes, L. / Mas, C. / Coute, Y. / Laurent, F. / Scherf, A. / Bougdour, A. / Hakimi, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q4a.cif.gz | 331.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q4a.ent.gz | 240.3 KB | Display | PDB format |
PDBx/mmJSON format | 7q4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q4a_validation.pdf.gz | 1001.2 KB | Display | wwPDB validaton report |
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Full document | 7q4a_full_validation.pdf.gz | 1011.5 KB | Display | |
Data in XML | 7q4a_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 7q4a_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/7q4a ftp://data.pdbj.org/pub/pdb/validation_reports/q4/7q4a | HTTPS FTP |
-Related structure data
Related structure data | 6cnhS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42877.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGGT1_313180 / Plasmid: pFastBac-1 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: S7UT92, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 27 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-SCN / | #6: Water | ChemComp-HOH / | |
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-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: 3.07 Å3/Da / Density % sol: 59.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 18% PEG 3350, 0.18 M Potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9655 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→48.62 Å / Num. obs: 45271 / % possible obs: 93.07 % / Redundancy: 4.5 % / Biso Wilson estimate: 55.45 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.37 |
Reflection shell | Resolution: 2.31→2.39 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 0.82 / Num. unique obs: 1688 / CC1/2: 0.357 / % possible all: 37.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CNH Resolution: 2.31→48.62 Å / SU ML: 0.3059 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.8033 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: 68.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→48.62 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: 20.2427251937 Å / Origin y: -29.2132043398 Å / Origin z: -7.44151070606 Å
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Refinement TLS group | Selection details: all |