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- PDB-4hzs: Crystal structure of Ack1 kinase domain with C-terminal SH3 domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hzs | ||||||
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Title | Crystal structure of Ack1 kinase domain with C-terminal SH3 domain | ||||||
![]() | Activated CDC42 kinase 1 | ||||||
![]() | TRANSFERASE / inactive state / allostery / dimerization / oligomerization / negative regulation / activation / phosphotransfer | ||||||
Function / homology | ![]() regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / cytoophidium / GTPase inhibitor activity / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / WW domain binding / clathrin-coated pit ...regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / cytoophidium / GTPase inhibitor activity / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / WW domain binding / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / adherens junction / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytoplasmic vesicle membrane / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / phosphorylation / histone H2AS1 kinase activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / intracellular membrane-bounded organelle / protein serine kinase activity / protein phosphorylation / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gajiwala, K.S. | ||||||
![]() | ![]() Title: Ack1: activation and regulation by allostery. Authors: Gajiwala, K.S. / Maegley, K. / Ferre, R. / He, Y.A. / Yu, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.6 KB | Display | ![]() |
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PDB format | ![]() | 207.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428 KB | Display | ![]() |
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Full document | ![]() | 464.2 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 43.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38861.527 Da / Num. of mol.: 4 Fragment: protein kinase and SH3 domains (UNP residues 115-453) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q07912, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.16 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2010 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.23→73.04 Å / Num. all: 34878 / Num. obs: 34878 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.187 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3.23→3.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2 / Num. unique all: 4895 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.8734 Å2 / ksol: 0.305827 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.23→73.04 Å
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Refine LS restraints |
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Refine LS restraints NCS | Weight Biso : 2 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.23→3.43 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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