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- PDB-3fyk: Crystal structure of a benzthiophene lead bound to MAPKAP Kinase-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fyk | ||||||
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Title | Crystal structure of a benzthiophene lead bound to MAPKAP Kinase-2 (MK-2) | ||||||
![]() | MAP kinase-activated protein kinase 2 | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kurumbail, R.G. / Caspers, N. | ||||||
![]() | ![]() Title: Benzothiophene inhibitors of MK2. Part 2: improvements in kinase selectivity and cell potency. Authors: Anderson, D.R. / Meyers, M.J. / Kurumbail, R.G. / Caspers, N. / Poda, G.I. / Long, S.A. / Pierce, B.S. / Mahoney, M.W. / Mourey, R.J. / Parikh, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.8 KB | Display | ![]() |
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PDB format | ![]() | 55.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 520.5 KB | Display | ![]() |
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Full document | ![]() | 535.3 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fyjC ![]() 3fz1C ![]() 1a06S ![]() 1atpS ![]() 1cdkS ![]() 2phkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Components
#1: Protein | Mass: 37897.750 Da / Num. of mol.: 1 / Fragment: MK-2 kinase module and the auto-inhibitory domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P49137, ![]() |
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#2: Chemical | ChemComp-B98 / ( |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.54 Å3/Da / Density % sol: 72.88 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: MK-2 protein at 5 mg/ml equilibrated against a well solution of 1.6 - 2.0 M Sodium malonate at pH 5.4, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Mar 2, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→30 Å / Num. obs: 8772 / % possible obs: 93.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.083 / Χ2: 0.998 / Net I/σ(I): 19.778 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1A06,1ATP,1CDK,2PHK Resolution: 3.5→30 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.277 / WRfactor Rwork: 0.24 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.792 / SU B: 27.133 / SU ML: 0.428 / SU Rfree: 0.568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.568 / 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 max: 146.41 Å2 / Biso mean: 98.046 Å2 / Biso min: 54.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.498→3.589 Å / Total num. of bins used: 20
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