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Yorodumi- PDB-4y8d: Crystal structure of Cyclin-G associated kinase (GAK) complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y8d | ||||||
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Title | Crystal structure of Cyclin-G associated kinase (GAK) complexed with selective 12i inhibitor | ||||||
Components |
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Keywords | TRANSFERASE / kinase / nanobody / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information 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 / negative regulation of neuron projection development / Clathrin-mediated endocytosis / presynapse / protein-folding chaperone binding / vesicle / non-specific serine/threonine protein kinase / intracellular membrane-bounded organelle / protein serine kinase activity / focal adhesion / 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: 2.1 Å | ||||||
Authors | Chaikuad, A. / Heroven, C. / Nowak, R. / De Jonghe, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Selective Inhibitors of Cyclin G Associated Kinase (GAK) as Anti-Hepatitis C Agents. Authors: Kovackova, S. / Chang, L. / Bekerman, E. / Neveu, G. / Barouch-Bentov, R. / Chaikuad, A. / Heroven, C. / Sala, M. / De Jonghe, S. / Knapp, S. / Einav, S. / Herdewijn, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y8d.cif.gz | 329.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y8d.ent.gz | 267.8 KB | Display | PDB format |
PDBx/mmJSON format | 4y8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/4y8d ftp://data.pdbj.org/pub/pdb/validation_reports/y8/4y8d | HTTPS FTP |
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-Related structure data
Related structure data | 4c58S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 38183.551 Da / Num. of mol.: 2 / Fragment: UNP residues 14-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GAK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 pRARE2 References: UniProt: O14976, non-specific serine/threonine protein kinase #2: Protein | Mass: 15085.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lama glama (llama) #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.75 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 9% Broad-molecular weight PEG Smears (BMW PEG smears), 0.1M MES pH 6.2, 0.15M calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 31, 2013 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.58 Å / Num. obs: 45797 / % possible obs: 94.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C58 Resolution: 2.1→43.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.053 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.194 / 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: 70.498 Å2
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Refine analyze | Luzzati coordinate error obs: 0.342 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→43.58 Å
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Refine LS restraints |
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