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Yorodumi- PDB-1u4d: Structure of the ACK1 Kinase Domain bound to Debromohymenialdisine -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u4d | ||||||
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Title | Structure of the ACK1 Kinase Domain bound to Debromohymenialdisine | ||||||
Components | Activated CDC42 kinase 1 | ||||||
Keywords | TRANSFERASE / Tyrosine Kinase | ||||||
Function / homology | Function and homology information regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity ...regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / 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 / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lougheed, J.C. / Chen, R.H. / Mak, P. / Stout, T.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the Cdc42-associated Tyrosine Kinase ACK1. Authors: Lougheed, J.C. / Chen, R.H. / Mak, P. / Stout, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u4d.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u4d.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 1u4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/1u4d ftp://data.pdbj.org/pub/pdb/validation_reports/u4/1u4d | HTTPS FTP |
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-Related structure data
Related structure data | 1u46SC 1u54C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33058.047 Da / Num. of mol.: 2 / Fragment: Kinase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACK1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf-9 / References: UniProt: Q07912, EC: 2.7.1.112 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.1 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: PEG 2000, sodium chloride, magnesium chloride, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.6 Å / Num. obs: 32292 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rsym value: 0.059 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.373 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB CODE 1U46 Resolution: 2.1→46.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.571 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20 /
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