+Open data
-Basic information
Entry | Database: PDB / ID: 8rdk | ||||||
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Title | Crystal structure of human Haspin (GSG2) kinase bound to MD420 | ||||||
Components | Serine/threonine-protein kinase haspin | ||||||
Keywords | TRANSFERASE / Haspin / Kinase / Inhibitor | ||||||
Function / homology | Function and homology information histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / chromosome / mitotic cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction ...histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / chromosome / mitotic cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / centrosome / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kraemer, A. / Defois, M. / Giraud, F. / Moreau, P. / Anizon, F. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2024 Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting. Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S. #1: Journal: Biorxiv / Year: 2024 Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rdk.cif.gz | 149.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rdk.ent.gz | 114.3 KB | Display | PDB format |
PDBx/mmJSON format | 8rdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/8rdk ftp://data.pdbj.org/pub/pdb/validation_reports/rd/8rdk | HTTPS FTP |
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-Related structure data
Related structure data | 8pvoC 8pvpC 9epvC 9epwC 9epyC 9epzC 9eq0C 9eq1C C: citing same article (ref.) |
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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
#1: Protein | Mass: 40711.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HASPIN, GSG2 / Production host: Escherichia coli (E. coli) References: UniProt: Q8TF76, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-YQT / Mass: 245.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11N3 / Feature type: SUBJECT OF INVESTIGATION |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 51% MPD 0.1M SPG 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 4, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 2→86.87 Å / Num. obs: 32717 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 2387 / CC1/2: 0.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→52.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.726 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.142 / 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: 39.312 Å2
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Refinement step | Cycle: 1 / Resolution: 2→52.01 Å
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