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- PDB-8p5j: Kinase domain of mutant human ULK1 in complex with compound WZ4003 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p5j | ||||||
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Title | Kinase domain of mutant human ULK1 in complex with compound WZ4003 | ||||||
![]() | Serine/threonine-protein kinase ULK1 | ||||||
![]() | TRANSFERASE / Autophagy / Unc-like 1 kinase | ||||||
Function / homology | ![]() omegasome membrane / neuron projection regeneration / regulation of protein lipidation / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / 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 ...omegasome membrane / neuron projection regeneration / regulation of protein lipidation / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / 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 / axon extension / phagophore assembly site / TBC/RABGAPs / reticulophagy / Macroautophagy / Receptor Mediated Mitophagy / response to starvation / cellular response to nutrient levels / autophagosome membrane / autophagosome assembly / autophagosome / regulation of macroautophagy / negative regulation of protein-containing complex assembly / positive regulation of autophagy / macroautophagy / Regulation of TNFR1 signaling / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Battista, T. / Semrau, M.S. / Heroux, A. / Lolli, G. / Storici, P. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structures of ULK1 in complex with KCGS compounds Authors: Battista, T. / Semrau, M.S. / Lolli, G. / Storici, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.4 KB | Display | ![]() |
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PDB format | ![]() | 185.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p5gC ![]() 8p5hC ![]() 8p5iC ![]() 8p5kC ![]() 8p5lC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 8 - 279 / Label seq-ID: 9 - 280
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
#1: Protein | Mass: 32121.098 Da / Num. of mol.: 2 / Mutation: R245A, E245A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75385, non-specific serine/threonine protein kinase #2: Chemical | Mass: 496.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29ClN6O3 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.08 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.164→63.281 Å / Num. obs: 47753 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.999 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.164→2.201 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2362 / CC1/2: 0.697 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.156 Å2
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Refinement step | Cycle: LAST / Resolution: 2.164→63.281 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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