[English] 日本語
Yorodumi- PDB-1wvw: Crystal structures of kinase domain of DAP kinase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wvw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structures of kinase domain of DAP kinase in complex with small molecular inhibitors | ||||||
Components | Death-associated protein kinase 1DAPK1 | ||||||
Keywords | TRANSFERASE / protein kinase / apoptosis | ||||||
Function / homology | Function and homology information 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 / calmodulin-dependent protein kinase activity / syntaxin-1 binding / regulation of NMDA receptor activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...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 / calmodulin-dependent protein kinase activity / syntaxin-1 binding / regulation of NMDA receptor activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / negative regulation of translation / postsynaptic density / protein autophosphorylation / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / GTP binding / negative regulation of apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ueda, Y. / Ogata, H. / Yamakawa, A. / Higuchi, Y. | ||||||
Citation | Journal: To be Published Title: Crystal structure of kinase domain of DAP kinase Authors: Ueda, Y. / Ogata, H. / Yamakawa, A. / Higuchi, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wvw.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wvw.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 1wvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wvw ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wvw | HTTPS FTP |
---|
-Related structure data
Related structure data | 1kobS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Plasmid: pET31 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53355, EC: 2.7.1.37 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9 Å |
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: 0.9 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.3577 Å2 / ksol: 0.337593 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.979 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.42 Å / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|