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Open data
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Basic information
Entry | Database: PDB / ID: 5y80 | ||||||
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Title | Complex structure of cyclin G-associated kinase with gefitinib | ||||||
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![]() | TRANSFERASE/IMMUNE SYSTEM / kinase / complex / TRANSFERASE-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() regulation of clathrin coat assembly / Golgi to lysosome transport / synaptic vesicle uncoating / protein localization to Golgi apparatus / clathrin coat disassembly / clathrin coat assembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding ...regulation of clathrin coat assembly / Golgi to lysosome transport / synaptic vesicle uncoating / protein localization to Golgi apparatus / clathrin coat disassembly / clathrin coat assembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding / Golgi Associated Vesicle Biogenesis / Golgi organization / chaperone cofactor-dependent protein refolding / intracellular transport / cyclin binding / receptor-mediated endocytosis / protein localization to plasma membrane / presynapse / negative regulation of neuron projection development / Clathrin-mediated endocytosis / protein-folding chaperone binding / vesicle / non-specific serine/threonine protein kinase / cell cycle / phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / perinuclear region of cytoplasm / Golgi apparatus / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ohbayashi, N. / Murayama, K. / Kato-Murayama, M. / Shirouzu, M. | ||||||
![]() | ![]() Title: Structural Basis for the Inhibition of Cyclin G-Associated Kinase by Gefitinib. Authors: Ohbayashi, N. / Murayama, K. / Kato-Murayama, M. / Kukimoto-Niino, M. / Uejima, T. / Matsuda, T. / Ohsawa, N. / Yokoyoma, S. / Nojima, H. / Shirouzu, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.2 KB | Display | ![]() |
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PDB format | ![]() | 76.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 940.3 KB | Display | ![]() |
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Full document | ![]() | 949.3 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5y7zC ![]() 4c57S S: Starting model for refinement C: citing same article ( |
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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: 35657.766 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O14976, non-specific serine/threonine protein kinase | ||
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#2: Antibody | Mass: 16189.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M ammonium sulfate,0.1 M sodium cacodylate trihydrate (pH 6.5), 15% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.7 Å / Num. obs: 17801 / % possible obs: 100 % / Redundancy: 9.3 % / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 1968 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4C57 Resolution: 2.5→44.924 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→44.924 Å
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Refine LS restraints |
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LS refinement shell |
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