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Open data
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Basic information
Entry | Database: PDB / ID: 4c57 | ||||||
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Title | Structure of GAK kinase in complex with a nanobody | ||||||
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![]() | TRANSFERASE / KINASE / CONFORMATIONAL PLASTICITY / ACTIVATION | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Chaikuad, A. / Keates, T. / Krojer, T. / Allerston, C.K. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Muller-Knapp, S. | ||||||
![]() | ![]() Title: Structure of Cyclin G-Associated Kinase (Gak) Trapped in Different Conformations Using Nanobodies. Authors: Chaikuad, A. / Keates, T. / Vincke, C. / Kaufholz, M. / Zenn, M. / Zimmermann, B. / Gutierrez, C. / Zhang, R. / Hatzos-Skintges, C. / Joachimiak, A. / Muyldermans, S. / Herberg, F.W. / Knapp, S. / Muller, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359.8 KB | Display | ![]() |
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PDB format | ![]() | 293.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1006.8 KB | Display | ![]() |
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Full document | ![]() | 1012.6 KB | Display | |
Data in XML | ![]() | 33.2 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c58C ![]() 4c59C ![]() 1op9S ![]() 3ll6 C: citing same article ( S: Starting model for refinement |
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Similar 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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Unit cell |
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Components
-Protein / Antibody , 2 types, 4 molecules ABCD
#1: Protein | Mass: 38183.551 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN RESIDUES 14-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O14976, non-specific serine/threonine protein kinase #2: Antibody | Mass: 15670.259 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 195 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FEF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FEF.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | SYNTHETIC, NON-BIOLOGICAL |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 7 Details: 14% PEG 3350, 0.2 M SODIUM SULFATE, 0.1 M BIS-TRIS PROPANE, PH 7.0, 10% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→83.39 Å / Num. obs: 34717 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 64.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LL6 AND 1OP9 Resolution: 2.55→74.68 Å / Cor.coef. Fo:Fc: 0.9439 / Cor.coef. Fo:Fc free: 0.9224 / SU R Cruickshank DPI: 0.455 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.432 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.261
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Displacement parameters | Biso mean: 79.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.422 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→74.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.63 Å / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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