+Open data
-Basic information
Entry | Database: PDB / ID: 4yc8 | ||||||
---|---|---|---|---|---|---|---|
Title | C-Helix-Out Binding of Dasatinib Analog to c-Abl Kinase | ||||||
Components | Tyrosine-protein kinase ABL1 | ||||||
Keywords | TRANSFERASE / Kinase / C-Helix-Out | ||||||
Function / homology | Function and homology information negative regulation of phospholipase C activity / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine ...negative regulation of phospholipase C activity / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / activation of protein kinase C activity / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of extracellular matrix organization / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of cell motility / regulation of axon extension / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / regulation of hematopoietic stem cell differentiation / syntaxin binding / cardiac muscle cell proliferation / HDR through Single Strand Annealing (SSA) / regulation of T cell differentiation / negative regulation of double-strand break repair via homologous recombination / positive regulation of cell migration involved in sprouting angiogenesis / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of cell-cell adhesion / Myogenesis / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / RUNX2 regulates osteoblast differentiation / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / Bergmann glial cell differentiation / associative learning / neuromuscular process controlling balance / regulation of endocytosis / actin monomer binding / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / mismatch repair / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of T cell migration / canonical NF-kappaB signal transduction / BMP signaling pathway / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / signal transduction in response to DNA damage / peptidyl-tyrosine autophosphorylation / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / cellular response to transforming growth factor beta stimulus / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / actin filament polymerization / SH2 domain binding / response to endoplasmic reticulum stress / phosphotyrosine residue binding / ephrin receptor binding / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / post-embryonic development / protein kinase C binding / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of endothelial cell migration / thymus development / regulation of autophagy / neural tube closure / integrin-mediated signaling pathway / establishment of localization in cell / regulation of actin cytoskeleton organization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Kwarcinski, F.E. / Brandvold, K.B. / Johnson, T.J. / Phadke, S. / Meagher, J.L. / Seeliger, M.A. / Stuckey, J.A. / Soellner, M.B. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity. Authors: Kwarcinski, F.E. / Brandvold, K.R. / Phadke, S. / Beleh, O.M. / Johnson, T.K. / Meagher, J.L. / Seeliger, M.A. / Stuckey, J.A. / Soellner, M.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yc8.cif.gz | 221.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yc8.ent.gz | 176 KB | Display | PDB format |
PDBx/mmJSON format | 4yc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/4yc8 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/4yc8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ybjC 4ybkC 2g1tS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33222.988 Da / Num. of mol.: 2 / Fragment: UNP residues 248-531 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) References: UniProt: P00519, non-specific protein-tyrosine kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.1 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 22% PEG 3350, 100 mM NaOAc |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 18959 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 54.09 Å2 / Rmerge(I) obs: 0.1 / Χ2: 1.022 / Net I/av σ(I): 22.174 / Net I/σ(I): 7.7 / Num. measured all: 134756 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2g1t Resolution: 2.9→47.32 Å / Cor.coef. Fo:Fc: 0.9092 / Cor.coef. Fo:Fc free: 0.8631 / SU R Cruickshank DPI: 2.004 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.506 / SU Rfree Blow DPI: 0.344 / SU Rfree Cruickshank DPI: 0.348
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.12 Å2 / Biso mean: 35.42 Å2 / Biso min: 3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.363 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→47.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Total num. of bins used: 9
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|