+Open data
-Basic information
Entry | Database: PDB / ID: 7azb | ||||||
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Title | Structure of DDR2 DS domain in complex with VHH | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Kinase / Extracellular domain / 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 / positive regulation of extracellular matrix disassembly / chondrocyte proliferation / positive regulation of hepatic stellate cell activation / endochondral bone growth / regulation of extracellular matrix disassembly / negative regulation of hydrogen peroxide-mediated programmed cell death / collagen-activated tyrosine kinase receptor signaling pathway ...positive regulation of hepatic stellate cell proliferation / protein tyrosine kinase collagen receptor activity / biomineral tissue development / positive regulation of extracellular matrix disassembly / chondrocyte proliferation / positive regulation of hepatic stellate cell activation / endochondral bone growth / regulation of extracellular matrix disassembly / negative regulation of hydrogen peroxide-mediated programmed cell death / collagen-activated tyrosine kinase receptor signaling pathway / regulation of bone mineralization / cellular response to angiotensin / positive regulation of fibroblast migration / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / regulation of tissue remodeling / positive regulation of wound healing / Non-integrin membrane-ECM interactions / positive regulation of collagen biosynthetic process / positive regulation of protein kinase activity / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of osteoblast differentiation / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / collagen binding / response to muscle stretch / transmembrane receptor protein tyrosine kinase activity / ossification / 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 / protein autophosphorylation / receptor complex / cell adhesion / apical plasma membrane / focal adhesion / negative regulation of apoptotic process / signal transduction / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Talagas, A. / Nawrotek, A. / Arrial, A. / Vuillard, L.M. / Miallau, L. | ||||||
Citation | Journal: To Be Published Title: Structure of DDR2 DS domain in complex with VHH Authors: Talagas, A. / Nawrotek, 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 | 7azb.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7azb.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 7azb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7azb_validation.pdf.gz | 439.4 KB | Display | wwPDB validaton report |
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Full document | 7azb_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 7azb_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 7azb_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/7azb ftp://data.pdbj.org/pub/pdb/validation_reports/az/7azb | HTTPS FTP |
-Related structure data
Related structure data | 2z4fS 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: 18899.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDR2, NTRKR3, TKT, TYRO10 / Production host: Drosophila melanogaster (fruit fly) References: UniProt: Q16832, receptor protein-tyrosine kinase |
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#2: Antibody | Mass: 16618.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: 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: 1.96 Å3/Da / Density % sol: 37.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium sulphate monohydrate, 20 % PEG3350 |
-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: 0.98009 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98009 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→54.77 Å / Num. obs: 8157 / % possible obs: 92.4 % / Redundancy: 10.9 % / CC1/2: 0.997 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.62→2.74 Å / Num. unique obs: 408 / CC1/2: 0.468 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z4F Resolution: 2.62→49.89 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.863 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.411
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Displacement parameters | Biso mean: 71.67 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→49.89 Å
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