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Yorodumi- PDB-1fpu: CRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MO... -
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-Basic information
Entry | Database: PDB / ID: 1fpu | ||||||
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Title | CRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MOLECULE INHIBITOR | ||||||
Components | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL | ||||||
Keywords | TRANSFERASE / kinase / kinase inhibitor / STI-571 / activation loop | ||||||
Function / homology | Function and homology information Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / circulatory system development / transitional one stage B cell differentiation / DN4 thymocyte differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change ...Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / circulatory system development / transitional one stage B cell differentiation / DN4 thymocyte differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to epinephrine / regulation of cellular senescence / regulation of modification of synaptic structure / positive regulation of extracellular matrix organization / delta-catenin binding / B cell proliferation involved in immune response / Regulation of actin dynamics for phagocytic cup formation / cerebellum morphogenesis / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / regulation of extracellular matrix organization / positive regulation of blood vessel branching / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / Myogenesis / regulation of Cdc42 protein signal transduction / activated T cell proliferation / regulation of axon extension / proline-rich region binding / positive regulation of dendrite development / myoblast proliferation / mitogen-activated protein kinase binding / alpha-beta T cell differentiation / syntaxin binding / cardiac muscle cell proliferation / regulation of T cell differentiation / negative regulation of double-strand break repair via homologous recombination / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / regulation of microtubule polymerization / B cell proliferation / cell leading edge / positive regulation of osteoblast proliferation / negative regulation of cellular senescence / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / Bergmann glial cell differentiation / negative regulation of long-term synaptic potentiation / associative learning / neuromuscular process controlling balance / platelet-derived growth factor receptor signaling pathway / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / endothelial cell migration / positive regulation of T cell migration / BMP signaling pathway / phagocytosis / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / signal transduction in response to DNA damage / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / ERK1 and ERK2 cascade / negative regulation of canonical NF-kappaB signal transduction / ruffle / cellular response to transforming growth factor beta stimulus / response to endoplasmic reticulum stress / positive regulation of establishment of T cell polarity / actin filament polymerization / phosphotyrosine residue binding / ephrin receptor binding / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / post-embryonic development / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of endothelial cell migration / thymus development / positive regulation of interleukin-2 production / canonical NF-kappaB signal transduction / establishment of localization in cell / SH2 domain binding / neural tube closure / integrin-mediated signaling pathway / protein kinase C binding / regulation of actin cytoskeleton organization / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / neuron differentiation / autophagy Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Schindler, T. / Bornmann, W. / Pellicena, P. / Miller, W.T. / Clarkson, B. / Kuriyan, J. | ||||||
Citation | Journal: Science / Year: 2000 Title: Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Authors: Schindler, T. / Bornmann, W. / Pellicena, P. / Miller, W.T. / Clarkson, B. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fpu.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fpu.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fpu ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fpu | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | There are two kinase molecules in the asymmetric unit. The biological assembly is a monomer. |
-Components
#1: Protein | Mass: 33743.523 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00520, EC: 2.7.1.112 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 4000, magnesium chloride, mes, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9393 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Sep 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→99 Å / Num. obs: 221636 / % possible obs: 98.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.216 / Num. unique all: 2190 / % possible all: 90.6 |
Reflection | *PLUS Num. obs: 24122 / Num. measured all: 221636 |
Reflection shell | *PLUS % possible obs: 90.6 % |
-Processing
Software |
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Refinement | Resolution: 2.4→99 Å / Stereochemistry target values: Engh & Huber Details: Tight, noncrystallographic restraints were utilized throughout the refinement so that the final r.m.s. deviation between the two molecules is 0.05 and 0.04 Angstrom for the N-terminal and ...Details: Tight, noncrystallographic restraints were utilized throughout the refinement so that the final r.m.s. deviation between the two molecules is 0.05 and 0.04 Angstrom for the N-terminal and the C-terminal lobes, respectively (excluding residues 229 to 337, 252, 262, 271, 294, 306, 404, 447, 450, 466, and 491, which were built in different conformations in the two molecules). The electron density map was significantly weaker for one of the two molecules in the asymmetric unit (chain ID B), and all the analysis (cf. primary citation) relied on the better-ordered one (chain ID A).
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Refinement step | Cycle: LAST / Resolution: 2.4→99 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 99 Å / Rfactor obs: 0.239 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 |