+Open data
-Basic information
Entry | Database: PDB / ID: 6qas | ||||||
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Title | Crystal structure of ULK1 in complexed with PF-03814735 | ||||||
Components | Serine/threonine-protein kinase ULK1 | ||||||
Keywords | TRANSFERASE / ULK1 / autophagy / ATG1 / kinase / inhibitor complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information omegasome membrane / regulation of protein lipidation / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / nucleophagy / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs ...omegasome membrane / regulation of protein lipidation / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / nucleophagy / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site / axon extension / reticulophagy / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / response to starvation / autophagosome membrane / cellular response to nutrient levels / autophagosome assembly / autophagosome / regulation of macroautophagy / negative regulation of protein-containing complex assembly / positive regulation of autophagy / Regulation of TNFR1 signaling / macroautophagy / peptidyl-threonine phosphorylation / protein localization / recycling endosome / small GTPase binding / autophagy / neuron projection development / GTPase binding / peptidyl-serine phosphorylation / mitochondrial outer membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / negative regulation of cell population proliferation / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / endoplasmic reticulum membrane / signal transduction / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 6qas.cif.gz | 247.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qas.ent.gz | 199.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/6qas ftp://data.pdbj.org/pub/pdb/validation_reports/qa/6qas | HTTPS FTP |
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-Related structure data
Related structure data | 6qatC 6qauC 6qavC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 8 - 279 / Label seq-ID: 12 - 283
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32400.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 References: UniProt: O75385, non-specific serine/threonine protein kinase |
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-Non-polymers , 6 types, 419 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: 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: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 2.8 M Ammonium sulfate, 0.1 M citrate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→47.47 Å / Num. obs: 63838 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6154 / CC1/2: 0.806 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WNO Resolution: 1.75→47.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.975 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.102 / 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: 31.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.206 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→47.47 Å
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Refine LS restraints |
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