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Yorodumi- PDB-4ek8: Crystal structure of the cdk2 in complex with thiazolylpyrimidine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ek8 | ||||||
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Title | Crystal structure of the cdk2 in complex with thiazolylpyrimidine inhibitor | ||||||
Components | Cyclin-dependent kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ALPHA AND BETA PROTEIN (A+B) / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kang, Y.N. / Stuckey, J.A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the cdk2 in complex with thiazolylpyrimidine inhibitor Authors: Kang, Y.N. / Stuckey, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ek8.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ek8.ent.gz | 105.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ek8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ek8_validation.pdf.gz | 932.5 KB | Display | wwPDB validaton report |
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Full document | 4ek8_full_validation.pdf.gz | 935.1 KB | Display | |
Data in XML | 4ek8_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 4ek8_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/4ek8 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/4ek8 | HTTPS FTP |
-Related 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: 34002.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: PFB1 / Cell line (production host): HIGH-FIVE / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Chemical | ChemComp-16K / |
#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: 2.05 Å3/Da / Density % sol: 39.86 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.8 Details: 15-20% PEG3350, 0.2M AMMONIUM ACETATE, 0.1M HEPES, pH 7.8, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 / Wavelength: 0.97857 Å | |||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2009 / Details: MIRRORS | |||||||||
Radiation | Monochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→500 Å / Num. all: 31569 / Num. obs: 31538 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 24.14 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.8 | |||||||||
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.477 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 30.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Total num. of bins used: 16
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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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