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- PDB-2qj2: A Mechanistic Basis for Converting a Receptor Tyrosine Kinase Ago... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qj2 | ||||||
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Title | A Mechanistic Basis for Converting a Receptor Tyrosine Kinase Agonist to an Antagonist | ||||||
![]() | Hepatocyte growth factor![]() | ||||||
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Function / homology | ![]() positive regulation of neuron projection regeneration / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / regulation of p38MAPK cascade / Drug-mediated inhibition of MET activation / MET activates STAT3 / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of myelination / MET interacts with TNS proteins / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tolbert, W.D. / Daugherty, J. / Gao, C.-F. / Xe, Q. / Miranti, C. / Gherardi, E. / Vande Woude, G. / Xu, H.E. | ||||||
![]() | ![]() Title: A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist Authors: Tolbert, W.D. / Daugherty, J. / Gao, C. / Xie, Q. / Miranti, C. / Gherardi, E. / Vande Woude, G. / Xu, H.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.2 KB | Display | ![]() |
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PDB format | ![]() | 71.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 309.9 KB | Display | ![]() |
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Full document | ![]() | 318.8 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qj4C ![]() 1nk1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is the dimer in the asymmetric unit. |
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Components
#1: Protein | ![]() Mass: 21159.236 Da / Num. of mol.: 2 / Fragment: residues 28-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.56 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 mM ammonium sulfate, 26-29% PEG 4000 (w/w), 100 mM Tris-HCl pH 8.0, 0.5 mM beta-octyl glucoside, and 5% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 20, 2004 / Details: monochromator Si 1 1 1 |
Radiation | Monochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→22.3 Å / Num. all: 28061 / Num. obs: 28061 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1004 / Rsym value: 0.37 / % possible all: 31.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1NK1 Resolution: 1.81→22.29 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 256166.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Refined to a maximum likelihood target using amplitudes.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.8867 Å2 / ksol: 0.446293 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→22.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.91 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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