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Yorodumi- PDB-5vdk: Crystal structure of human WEE2 kinase domain in complex with MK1775 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vdk | ||||||
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Title | Crystal structure of human WEE2 kinase domain in complex with MK1775 | ||||||
Components | Wee1-like protein kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / WEE2 / TRANSFERASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information female pronucleus assembly / regulation of meiosis I / negative regulation of oocyte maturation / mitotic cell cycle checkpoint signaling / regulation of fertilization / female meiotic nuclear division / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of phosphorylation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity ...female pronucleus assembly / regulation of meiosis I / negative regulation of oocyte maturation / mitotic cell cycle checkpoint signaling / regulation of fertilization / female meiotic nuclear division / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of phosphorylation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / protein kinase activity / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Zhu, J.-Y. / Schonbrunn, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2017 Title: Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors. Authors: Zhu, J.Y. / Cuellar, R.A. / Berndt, N. / Lee, H.E. / Olesen, S.H. / Martin, M.P. / Jensen, J.T. / Georg, G.I. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vdk.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vdk.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/5vdk ftp://data.pdbj.org/pub/pdb/validation_reports/vd/5vdk | HTTPS FTP |
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-Related structure data
Related structure data | 5v5yC 5vc3C 5vc4C 5vc5C 5vc6C 5vcvC 5vcwC 5vcxC 5vcyC 5vczC 5vd0C 5vd1C 5vd2C 5vd3C 1x8bS C: citing same article (ref.) 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: 33071.246 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 202-492 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WEE2, WEE1B / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIPL References: UniProt: P0C1S8, non-specific protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-8X7 / | ||
#3: Chemical | #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: 2.4 Å3/Da / Density % sol: 48.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 14 MG/ML WEE2, 25 mM TRIS PH 8.0, 1 mM DTT, 0.2 M ammonium phosphate monobasic, 1.5 mM MK1775 |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 14, 2015 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→18.794 Å / Num. obs: 8422 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.374 % / Biso Wilson estimate: 46.12 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.109 / Χ2: 1.006 / Net I/σ(I): 12.39 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X8B Resolution: 2.7→18.794 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 32.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→18.794 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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