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Yorodumi- PDB-8fe9: Crystal structure of Ack1 kinase K161Q mutant in complex with the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fe9 | ||||||||||||
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Title | Crystal structure of Ack1 kinase K161Q mutant in complex with the selective inhibitor (R)-9b | ||||||||||||
Components | Activated CDC42 kinase 1 | ||||||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / tyrosine kinase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / WW domain binding / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / clathrin-coated pit ...regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / WW domain binding / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / phosphorylation / adherens junction / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytoplasmic vesicle membrane / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / endosome / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||||||||
Authors | Paung, Y. / Kan, Y. / Seeliger, M.S. / Miller, W.T. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biochemistry / Year: 2023 Title: Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk. Authors: Kan, Y. / Paung, Y. / Kim, Y. / Seeliger, M.A. / Miller, W.T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fe9.cif.gz | 149.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fe9.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 8fe9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fe9_validation.pdf.gz | 707.5 KB | Display | wwPDB validaton report |
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Full document | 8fe9_full_validation.pdf.gz | 710.4 KB | Display | |
Data in XML | 8fe9_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 8fe9_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/8fe9 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/8fe9 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32437.344 Da / Num. of mol.: 1 / Mutation: K161Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNK2, ACK1 / Plasmid: pFASTBAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary References: UniProt: Q07912, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-R9B / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.05 M Bis-Tris (pH 5.8), 19% PEG3350, 0.3 M MgCl2, 2.5% glycerol PH range: 6.0-6.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→28.99 Å / Num. obs: 7020 / % possible obs: 99 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 3.2→3.28 Å / Rmerge(I) obs: 1.088 / Num. unique obs: 624 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→28.99 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0648 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→28.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 33.8745121239 Å / Origin y: 18.4514654772 Å / Origin z: 24.6697009095 Å
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Refinement TLS group | Selection details: all |