+Open data
-Basic information
Entry | Database: PDB / ID: 7aym | ||||||
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Title | Structure of DDR2 Kinase domain in complex with IBZ3 | ||||||
Components | Discoidin domain-containing receptor 2,Epithelial discoidin domain-containing receptor 1 | ||||||
Keywords | MEMBRANE PROTEIN / Kinase / Receptor Tyrosine kinase Discoidin domain-containing receptor 2 / collagen / signal transduction / cell communication | ||||||
Function / homology | Function and homology information positive regulation of hepatic stellate cell proliferation / protein tyrosine kinase collagen receptor activity / biomineral tissue development / smooth muscle cell-matrix adhesion / positive regulation of extracellular matrix disassembly / chondrocyte proliferation / positive regulation of hepatic stellate cell activation / endochondral bone growth / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion ...positive regulation of hepatic stellate cell proliferation / protein tyrosine kinase collagen receptor activity / biomineral tissue development / smooth muscle cell-matrix adhesion / positive regulation of extracellular matrix disassembly / chondrocyte proliferation / positive regulation of hepatic stellate cell activation / endochondral bone growth / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / negative regulation of hydrogen peroxide-mediated programmed cell death / collagen-activated tyrosine kinase receptor signaling pathway / regulation of bone mineralization / positive regulation of fibroblast migration / cellular response to angiotensin / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / branching involved in mammary gland duct morphogenesis / regulation of tissue remodeling / wound healing, spreading of cells / smooth muscle cell migration / neuron projection extension / positive regulation of wound healing / axon development / Non-integrin membrane-ECM interactions / positive regulation of collagen biosynthetic process / positive regulation of protein kinase activity / mammary gland alveolus development / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of osteoblast differentiation / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / response to muscle stretch / lactation / embryo implantation / transmembrane receptor protein tyrosine kinase activity / ossification / regulation of cell growth / receptor protein-tyrosine kinase / positive regulation of DNA-binding transcription factor activity / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / actin cytoskeleton / cellular response to hypoxia / cell population proliferation / protein autophosphorylation / receptor complex / cell adhesion / apical plasma membrane / negative regulation of cell population proliferation / focal adhesion / negative regulation of apoptotic process / signal transduction / 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: 2.12 Å | ||||||
Authors | Nawrotek, A. / Talagas, A. / Vuillard, L.M. / Miallau, L. | ||||||
Citation | Journal: To Be Published Title: Structure of DDR2 Kinase domain in complex with IBZ3 Authors: Nawrotek, A. / Talagas, A. / Vuillard, L.M. / Miallau, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aym.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aym.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 7aym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aym_validation.pdf.gz | 679.4 KB | Display | wwPDB validaton report |
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Full document | 7aym_full_validation.pdf.gz | 683.3 KB | Display | |
Data in XML | 7aym_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 7aym_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/7aym ftp://data.pdbj.org/pub/pdb/validation_reports/ay/7aym | HTTPS FTP |
-Related structure data
Related structure data | 4bkjS 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: 38627.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: DDR2, NTRKR3, TKT, TYRO10, DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q16832, UniProt: Q08345, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-4VD / |
#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: 2.07 Å3/Da / Density % sol: 40.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2 M tri-sodium citrate, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980119 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980119 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→61.78 Å / Num. obs: 9068 / % possible obs: 88.6 % / Redundancy: 6.5 % / CC1/2: 0.988 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.09→2.436 Å / Num. unique obs: 453 / CC1/2: 0.772 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BKJ Resolution: 2.12→61.78 Å / Cor.coef. Fo:Fc: 0.856 / Cor.coef. Fo:Fc free: 0.781 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.383
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Displacement parameters | Biso mean: 26.24 Å2
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Refine analyze | Luzzati coordinate error obs: 0.48 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→61.78 Å
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