+Open data
-Basic information
Entry | Database: PDB / ID: 2hda | ||||||
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Title | Yes SH3 domain | ||||||
Components | Proto-oncogene tyrosine-protein kinase Yes | ||||||
Keywords | TRANSFERASE / main beta | ||||||
Function / homology | Function and homology information regulation of glucose transmembrane transport / protein modification process => GO:0036211 / regulation of vascular permeability / CD28 co-stimulation / EPH-Ephrin signaling / microtubule organizing center / epidermal growth factor receptor binding / Regulation of KIT signaling / postsynaptic specialization, intracellular component / CTLA4 inhibitory signaling ...regulation of glucose transmembrane transport / protein modification process => GO:0036211 / regulation of vascular permeability / CD28 co-stimulation / EPH-Ephrin signaling / microtubule organizing center / epidermal growth factor receptor binding / Regulation of KIT signaling / postsynaptic specialization, intracellular component / CTLA4 inhibitory signaling / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / cellular response to platelet-derived growth factor stimulus / RUNX2 regulates osteoblast differentiation / PECAM1 interactions / FCGR activation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / cellular response to retinoic acid / peptidyl-tyrosine autophosphorylation / extrinsic component of cytoplasmic side of plasma membrane / Signaling by ERBB2 / cellular response to transforming growth factor beta stimulus / EPHB-mediated forward signaling / T cell costimulation / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / actin filament / Regulation of signaling by CBL / FCGR3A-mediated phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / positive regulation of peptidyl-tyrosine phosphorylation / regulation of cell population proliferation / protein tyrosine kinase activity / transmembrane transporter binding / cell differentiation / signaling receptor binding / focal adhesion / innate immune response / glutamatergic synapse / Golgi apparatus / enzyme binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Camara-Artigas, A. / Luque, I. / Ruiz-Sanz, J. / Mateo, P.L. / Martin-Garcia, J.M. | ||||||
Citation | Journal: Febs Lett. / Year: 2007 Title: Crystallographic structure of the SH3 domain of the human c-Yes tyrosine kinase: Loop flexibility and amyloid aggregation. Authors: Martin-Garcia, J.M. / Luque, I. / Mateo, P.L. / Ruiz-Sanz, J. / Camara-Artigas, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hda.cif.gz | 25.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hda.ent.gz | 16.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/2hda ftp://data.pdbj.org/pub/pdb/validation_reports/hd/2hda | HTTPS FTP |
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-Related structure data
Related structure data | 1fynS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7128.813 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YES1, YES / Production host: Escherichia coli (E. coli) References: UniProt: P07947, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-SO4 / |
#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: 1.99 Å3/Da / Density % sol: 38.19 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.6 M ammonium sulphate, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 15K, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Jan 30, 2006 / Details: Montel optics |
Radiation | Monochromator: Bruker Microfocus (Montel Optics) Microstar / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. obs: 5626 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.08 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.0469 / Rsym value: 0.025 / Net I/σ(I): 28.37 |
Reflection shell | Resolution: 1.81→1.95 Å / Redundancy: 4.19 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 5.19 / Num. unique all: 1058 / Rsym value: 0.1825 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FYN Resolution: 1.9→14.86 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / SU B: 2.452 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.186 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→14.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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