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Yorodumi- PDB-3wbl: Crystal structure of CDK2 in complex with pyrazolopyrimidine inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wbl | ||||||
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Title | Crystal structure of CDK2 in complex with pyrazolopyrimidine inhibitor | ||||||
Components | Cyclin-dependent kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Binding Sites / Tumor / Cyclin-Dependent Kinase 2 / Drug Design / MAP Kinase Kinase 2 / MK2 / Protein Kinase Inhibitors / Pyrazoles / Pyrimidines / Structure-Activity Relationship / 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: 2 Å | ||||||
Authors | Fujino, A. / Fukushima, K. / Kubota, T. / Kosugi, T. / Takimoto-Kamimura, M. | ||||||
Citation | Journal: J.SYNCHROTRON RADIAT. / Year: 2013 Title: Crystal structure of human cyclin-dependent kinase-2 complex with MK2 inhibitor TEI-I01800: insight into the selectivity. Authors: Fujino, A. / Fukushima, K. / Kubota, T. / Kosugi, T. / Takimoto-Kamimura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wbl.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wbl.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wbl_validation.pdf.gz | 704.3 KB | Display | wwPDB validaton report |
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Full document | 3wbl_full_validation.pdf.gz | 708.7 KB | Display | |
Data in XML | 3wbl_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 3wbl_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/3wbl ftp://data.pdbj.org/pub/pdb/validation_reports/wb/3wbl | HTTPS FTP |
-Related structure data
Related structure data | 1fvtS 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: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tn5 / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-PDY / |
#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: 2.07 Å3/Da / Density % sol: 40.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG3350, Ammonium Acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 25, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 19621 / Num. obs: 19590 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.03 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.23 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 8.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FVT Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 3.731 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.183 / 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: 22.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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