+
Open data
-
Basic information
Entry | Database: PDB / ID: 2hda | ||||||
---|---|---|---|---|---|---|---|
Title | Yes SH3 domain | ||||||
![]() | Proto-oncogene tyrosine-protein kinase Yes | ||||||
![]() | TRANSFERASE / main beta | ||||||
Function / homology | ![]() regulation of glucose transmembrane transport / protein modification process => GO:0036211 / regulation of vascular permeability / CD28 co-stimulation / EPH-Ephrin signaling / microtubule organizing center / Regulation of KIT signaling / epidermal growth factor receptor binding / 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 / Regulation of KIT signaling / epidermal growth factor receptor binding / 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 / peptidyl-tyrosine autophosphorylation / extrinsic component of cytoplasmic side of plasma membrane / PECAM1 interactions / Signaling by ERBB2 / FCGR activation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / cellular response to retinoic acid / cell surface receptor protein tyrosine kinase signaling pathway / cellular response to transforming growth factor beta stimulus / T cell costimulation / EPHB-mediated forward signaling / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / actin filament / Regulation of signaling by CBL / FCGR3A-mediated phagocytosis / 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 / innate immune response / focal adhesion / signaling receptor binding / glutamatergic synapse / enzyme binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Camara-Artigas, A. / Luque, I. / Ruiz-Sanz, J. / Mateo, P.L. / Martin-Garcia, J.M. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 25.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 16.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1fynS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 | ![]()
| x 6||||||||||||||||||
3 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-
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.) ![]() ![]() ![]() References: UniProt: P07947, non-specific protein-tyrosine kinase |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.19 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→14.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|