+Open data
-Basic information
Entry | Database: PDB / ID: 4c58 | ||||||
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Title | Structure of GAK kinase in complex with nanobody (NbGAK_4) | ||||||
Components |
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Keywords | TRANSFERASE / KINASE / CONFORMATIONAL PLASTICITY / ACTIVATION | ||||||
Function / homology | Function and homology information regulation of clathrin coat assembly / synaptic vesicle uncoating / Golgi to lysosome transport / protein localization to Golgi apparatus / clathrin coat assembly / clathrin coat disassembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding ...regulation of clathrin coat assembly / synaptic vesicle uncoating / Golgi to lysosome transport / protein localization to Golgi apparatus / clathrin coat assembly / clathrin coat disassembly / clathrin-dependent endocytosis / endoplasmic reticulum organization / clathrin-coated vesicle / clathrin binding / Golgi Associated Vesicle Biogenesis / Golgi organization / chaperone cofactor-dependent protein refolding / intracellular transport / receptor-mediated endocytosis / cyclin binding / protein localization to plasma membrane / negative regulation of neuron projection development / presynapse / Clathrin-mediated endocytosis / protein-folding chaperone binding / vesicle / non-specific serine/threonine protein kinase / cell cycle / phosphorylation / focal adhesion / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / perinuclear region of cytoplasm / Golgi apparatus / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Chaikuad, A. / Keates, T. / Allerston, C.K. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Muller-Knapp, S. | ||||||
Citation | Journal: Biochem. J. / Year: 2014 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.G. / Hatzos-Skintges, C. / Joachimiak, A. / Muyldermans, S. / Herberg, F.W. / Knapp, S. / Muller, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c58.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c58.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 4c58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/4c58 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/4c58 | HTTPS FTP |
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-Related structure data
Related structure data | 4c57C 4c59C 1op9S 3ll6 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38183.551 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 27-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GAK / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 References: UniProt: O14976, non-specific serine/threonine protein kinase | ||||||
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#2: Protein | Mass: 15085.511 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) | ||||||
#3: Chemical | #4: Chemical | ChemComp-824 / | #5: Water | ChemComp-HOH / | Sequence details | SYNTHETIC, NON-BIOLOGICAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 12% PEG 3350, 0.13 M MAGNESIUM FORMATE, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0121 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 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: 1.0121 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→45.09 Å / Num. obs: 22748 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.16→2.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3LL6 AND 1OP9 Resolution: 2.16→38.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.053 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.243 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→38.38 Å
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