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- PDB-1wvw: Crystal structures of kinase domain of DAP kinase in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wvw | ||||||
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Title | Crystal structures of kinase domain of DAP kinase in complex with small molecular inhibitors | ||||||
![]() | Death-associated protein kinase 1![]() | ||||||
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Function / homology | ![]() cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ueda, Y. / Ogata, H. / Yamakawa, A. / Higuchi, Y. | ||||||
![]() | ![]() Title: Crystal structure of kinase domain of DAP kinase Authors: Ueda, Y. / Ogata, H. / Yamakawa, A. / Higuchi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.1 KB | Display | ![]() |
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PDB format | ![]() | 48.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kobS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 31981.500 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63 % |
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Crystal grow![]() | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: sodium cacodylate, PEG8000, magnesium acetate, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→20 Å / Num. all: 17286 / Num. obs: 17268 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.118 |
Reflection shell | Resolution: 2.4→2.53 Å / Rmerge(I) obs: 0.346 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1kob Resolution: 2.4→19.979 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1036676.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.3577 Å2 / ksol: 0.337593 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.979 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.42 Å / Total num. of bins used: 6
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Xplor file |
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