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Open data
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Basic information
Entry | Database: PDB / ID: 4fub | ||||||
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Title | Crystal Structure of the Urokinase | ||||||
![]() | Urokinase-type plasminogen activator | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kang, Y.N. / Stuckey, J.A. / Nienaber, V. / Giranda, V. | ||||||
![]() | ![]() Title: Crystal Structure of the Urokinase Authors: Kang, Y.N. / Stuckey, J.A. / Nienaber, V. / Giranda, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.8 KB | Display | ![]() |
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PDB format | ![]() | 91 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4fu7C ![]() 4fu8C ![]() 4fu9C ![]() 4fucC ![]() 4fudC ![]() 4fueC ![]() 4fufC ![]() 4fugC ![]() 4fuhC ![]() 4fuiC ![]() 4fujC 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27715.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 259 molecules ![](data/chem/img/4UP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/15P.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/15P.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-4UP / | ||||||
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#3: Chemical | ChemComp-SO4 / | ||||||
#4: Chemical | ChemComp-SIN / | ||||||
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-15P / | #7: Chemical | ChemComp-ACT / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.15 M Li2SO4, 20% polyethylene glycol MW 4000 in succinate buffer, pH 4.8-6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K PH range: 4.8-6.0 |
-Data collection
Diffraction | Mean temperature: 160 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→40 Å / % possible obs: 86.3 % / Rmerge(I) obs: 0.122 / Χ2: 1.259 / Net I/σ(I): 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso max: 70.11 Å2 / Biso mean: 18.5997 Å2 / Biso min: 6.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.164 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→17.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: -13.7272 Å / Origin y: -9.4447 Å / Origin z: 10.9941 Å
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Refinement TLS group | Selection details: { A|1 - A|246 } |