+Open data
-Basic information
Entry | Database: PDB / ID: 6qav | ||||||
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Title | Crystal structure of ULK2 in complexed with MRT68921 | ||||||
Components | Serine/threonine-protein kinase ULK2 | ||||||
Keywords | TRANSFERASE / ULK2 / autophagy / kinase / inhibitor complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information negative regulation of collateral sprouting / collateral sprouting / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / axon extension / phagophore assembly site / reticulophagy / response to starvation / autophagosome assembly / autophagosome ...negative regulation of collateral sprouting / collateral sprouting / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / axon extension / phagophore assembly site / reticulophagy / response to starvation / autophagosome assembly / autophagosome / positive regulation of autophagy / cytoplasmic vesicle membrane / autophagy / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Chaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Biochem.J. / Year: 2019 Title: Conservation of structure, function and inhibitor binding in UNC-51-like kinase 1 and 2 (ULK1/2). Authors: Chaikuad, A. / Koschade, S.E. / Stolz, A. / Zivkovic, K. / Pohl, C. / Shaid, S. / Ren, H. / Lambert, L.J. / Cosford, N.D.P. / Brandts, C.H. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qav.cif.gz | 450.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qav.ent.gz | 373.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qav_validation.pdf.gz | 1001.6 KB | Display | wwPDB validaton report |
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Full document | 6qav_full_validation.pdf.gz | 1011.8 KB | Display | |
Data in XML | 6qav_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 6qav_validation.cif.gz | 60.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/6qav ftp://data.pdbj.org/pub/pdb/validation_reports/qa/6qav | HTTPS FTP |
-Related structure data
Related structure data | 6qasC 6qatC 6qauC 4wnoS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 31767.721 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ULK2, KIAA0623 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 References: UniProt: Q8IYT8, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 379 molecules
#2: Chemical | ChemComp-HVH / ~{ #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.15 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 37.5% PEG 3350, 0.1 M sodium citrate, pH 5.9, 0.15 M MgCl2, 0.1 M bis-tris, pH 5.5, 5% glycerol PH range: 5.5-5.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→57.97 Å / Num. obs: 68365 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6706 / CC1/2: 0.842 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WNO Resolution: 2.05→57.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.057 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.181 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.569 Å2
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Refine analyze | Luzzati coordinate error obs: 0.292 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.05→57.97 Å
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Refine LS restraints |
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