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Yorodumi- PDB-4ckr: Crystal structure of the human DDR1 kinase domain in complex with... -
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-Basic information
Entry | Database: PDB / ID: 4ckr | |||||||||
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Title | Crystal structure of the human DDR1 kinase domain in complex with DDR1-IN-1 | |||||||||
Components | EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1 | |||||||||
Keywords | TRANSFERASE / COLLAGEN / DISCOIDIN DOMAIN | |||||||||
Function / homology | Function and homology information protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension ...protein tyrosine kinase collagen receptor activity / smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension / axon development / Non-integrin membrane-ECM interactions / mammary gland alveolus development / peptidyl-tyrosine autophosphorylation / embryo implantation / collagen binding / lactation / transmembrane receptor protein tyrosine kinase activity / regulation of cell growth / positive regulation of neuron projection development / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / cell population proliferation / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell adhesion / negative regulation of cell population proliferation / extracellular space / extracellular exosome / ATP binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Canning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Krojer, T. / Newman, J.A. / Dixon-Clarke, S. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. ...Canning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Krojer, T. / Newman, J.A. / Dixon-Clarke, S. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. | |||||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Discovery of a Potent and Selective Ddr1 Receptor Tyrosine Kinase Inhibitor. Authors: Kim, H. / Tan, L. / Weisberg, E.L. / Liu, F. / Canning, P. / Choi, H.G. / Ezell, S.A. / Wu, H. / Zhao, Z. / Wang, J. / Mandinova, A. / Griffin, J.D. / Bullock, A.N. / Liu, Q. / Lee, S.W. / Gray, N.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ckr.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ckr.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ckr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/4ckr ftp://data.pdbj.org/pub/pdb/validation_reports/ck/4ckr | HTTPS FTP |
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-Related structure data
Related structure data | 3zosS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35754.094 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 601-913 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q08345, receptor protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-DI1 / | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | Details: 21% PEG3350, 0.1M BIS-TRIS-PROPANE PH 7.2, 0.2M SODIUM/POTASSIUM PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.4 Å / Num. obs: 17062 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZOS Resolution: 2.2→49.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.947 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.173 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.4 Å
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