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Yorodumi- PDB-4bkj: Crystal structure of the human DDR1 kinase domain in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bkj | ||||||
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Title | Crystal structure of the human DDR1 kinase domain in complex with imatinib | ||||||
Components | EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1 | ||||||
Keywords | TRANSFERASE / RECEPTOR / RTK / COLLAGEN / DISCOIDIN DOMAIN / RECEPTOR TYROSINE KINASE | ||||||
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 / peptidyl-tyrosine autophosphorylation / Non-integrin membrane-ECM interactions / mammary gland alveolus development / transmembrane receptor protein tyrosine kinase activity / collagen binding / lactation / embryo implantation / regulation of cell growth / receptor protein-tyrosine kinase / positive regulation of neuron projection development / protein autophosphorylation / receptor complex / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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: 1.7 Å | ||||||
Authors | Canning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Krojer, T. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Structural Mechanisms Determining Inhibition of the Collagen Receptor Ddr1 by Selective and Multi-Targeted Type II Kinase Inhibitors Authors: Canning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Krojer, T. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bkj.cif.gz | 258.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bkj.ent.gz | 208.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bkj_validation.pdf.gz | 878.7 KB | Display | wwPDB validaton report |
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Full document | 4bkj_full_validation.pdf.gz | 884.8 KB | Display | |
Data in XML | 4bkj_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 4bkj_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bkj ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bkj | HTTPS FTP |
-Related structure data
Related structure data | 3zosSC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 600 - 913 / Label seq-ID: 2 - 315
NCS oper: (Code: given Matrix: (-0.0158, 0.9999, 0.0039), Vector: |
-Components
#1: Protein | Mass: 35754.094 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESDIUES 564-876 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 #2: Chemical | #3: Chemical | ChemComp-EDO / #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: 2.28 Å3/Da / Density % sol: 46.11 % / Description: NONE |
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Crystal grow | Details: 0.1M BIS-TRIS PH 6.3, 34% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.7→45.14 Å / Num. obs: 72847 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZOS Resolution: 1.7→45.14 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.745 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.018 / 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: 25.117 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→45.14 Å
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Refine LS restraints |
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