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Yorodumi- PDB-8p5i: Kinase domain of mutant human ULK1 in complex with compound XMD-17-51 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p5i | ||||||
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Title | Kinase domain of mutant human ULK1 in complex with compound XMD-17-51 | ||||||
Components | Serine/threonine-protein kinase ULK1 | ||||||
Keywords | TRANSFERASE / Autophagy / Unc-like 1 kinase | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.829 Å | ||||||
Authors | Battista, T. / Semrau, M.S. / Heroux, A. / Lolli, G. / Storici, P. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p5i.cif.gz | 476.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p5i.ent.gz | 385.4 KB | Display | PDB format |
PDBx/mmJSON format | 8p5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p5i_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8p5i_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8p5i_validation.xml.gz | 51.7 KB | Display | |
Data in CIF | 8p5i_validation.cif.gz | 75.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/8p5i ftp://data.pdbj.org/pub/pdb/validation_reports/p5/8p5i | HTTPS FTP |
-Related structure data
Related structure data | 8p5gC 8p5hC 8p5jC 8p5kC 8p5lC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: THR / Beg label comp-ID: THR / Auth asym-ID: A / Label asym-ID: A
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 32121.098 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Production host: Escherichia coli (E. coli) References: UniProt: O75385, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 976 molecules
#2: Chemical | ChemComp-WYX / Mass: 404.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H24N8O / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.51 Å3/Da / Density % sol: 64.98 % |
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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: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
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: 1.829→96.402 Å / Num. obs: 156366 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.829→1.86 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7774 / CC1/2: 0.723 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.829→96.402 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.241 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.092 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: 30.298 Å2
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Refinement step | Cycle: LAST / Resolution: 1.829→96.402 Å
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Refine LS restraints |
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