+Open data
-Basic information
Entry | Database: PDB / ID: 5jq8 | ||||||
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Title | Crystal structure of CDK2 in complex with inhibitor ICEC0943 | ||||||
Components | Cyclin-dependent kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase inhibitor / 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 / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Hazel, P. / Freemont, P.S. | ||||||
Citation | Journal: ChemMedChem / Year: 2017 Title: Inhibitor Selectivity for Cyclin-Dependent Kinase 7: A Structural, Thermodynamic, and Modelling Study. Authors: Hazel, P. / Kroll, S.H. / Bondke, A. / Barbazanges, M. / Patel, H. / Fuchter, M.J. / Coombes, R.C. / Ali, S. / Barrett, A.G. / Freemont, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jq8.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jq8.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jq8_validation.pdf.gz | 767.1 KB | Display | wwPDB validaton report |
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Full document | 5jq8_full_validation.pdf.gz | 770.3 KB | Display | |
Data in XML | 5jq8_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 5jq8_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/5jq8 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/5jq8 | HTTPS FTP |
-Related structure data
Related structure data | 5jq5C 3ns9S S: Starting model for refinement C: citing same article (ref.) |
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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: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Chemical | ChemComp-I73 / ( |
#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: 2.04 Å3/Da / Density % sol: 39.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1M AMMONIUM ACETATE, PH 7.8, 6% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50.79 Å / Num. obs: 20808 / % possible obs: 98.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.94→2.05 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.5 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NS9 Resolution: 1.94→50.79 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.893 / SU B: 4.196 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.182 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.828 Å2
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Refinement step | Cycle: 1 / Resolution: 1.94→50.79 Å
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Refine LS restraints |
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