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Yorodumi- PDB-5fdx: Structure of DDR1 receptor tyrosine kinase in complex with D2164 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fdx | ||||||
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Title | Structure of DDR1 receptor tyrosine kinase in complex with D2164 inhibitor at 2.65 Angstroms resolution. | ||||||
Components | Epithelial discoidin domain-containing receptor 1 | ||||||
Keywords | TRANSFERASE / DDR1 Kinase / inhibitors / Structural Genomics / PSI-Biology / Structural Genomics Consortium / SGC | ||||||
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: 2.65 Å | ||||||
Authors | Bartual, S.G. / Pinkas, D.M. / Wang, Z. / Ding, K. / Mahajan, P. / Kupinska, K. / Mukhopadhyay, S. / Strain-Damerell, C. / Chalk, R. / Borkowska, O. ...Bartual, S.G. / Pinkas, D.M. / Wang, Z. / Ding, K. / Mahajan, P. / Kupinska, K. / Mukhopadhyay, S. / Strain-Damerell, C. / Chalk, R. / Borkowska, O. / Talon, R. / Kopec, J. / Williams, E. / Tallant, C. / Chaikuad, A. / Sorell, F. / Newman, J. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Structure of DDR1 receptor tyrosine kinase in complex with D2164 inhibitor at 2.65 Angstroms resolution. Authors: Bartual, S.G. / Ding, K. / Wang, Z. / Bullock, N.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fdx.cif.gz | 239.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fdx.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fdx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fdx_validation.pdf.gz | 959.9 KB | Display | wwPDB validaton report |
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Full document | 5fdx_full_validation.pdf.gz | 969.3 KB | Display | |
Data in XML | 5fdx_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 5fdx_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fdx ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fdx | HTTPS FTP |
-Related structure data
Related structure data | 4ckrS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38282.805 Da / Num. of mol.: 2 / Fragment: UNP Residues 601-913 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q08345, receptor protein-tyrosine kinase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH6.5 0.2M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92818 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→43.44 Å / Num. obs: 19393 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 54.08 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.072 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 0.8 / Rpim(I) all: 0.629 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CKR Resolution: 2.65→43.44 Å / Cor.coef. Fo:Fc: 0.9196 / Cor.coef. Fo:Fc free: 0.8647 / SU R Cruickshank DPI: 1.058 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.921 / SU Rfree Blow DPI: 0.344 / SU Rfree Cruickshank DPI: 0.352
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Displacement parameters | Biso mean: 58.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.381 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→43.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.79 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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