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- PDB-5lhq: The EGR-cmk active site inhibited catalytic domain of murine urok... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lhq | |||||||||||||||
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Title | The EGR-cmk active site inhibited catalytic domain of murine urokinase-type plasminogen activator in complex with the allosteric inhibitory nanobody Nb7 | |||||||||||||||
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![]() | Hydrolase/Antibody / Trypsin-like serine proteases / Nanobody / Inhibitor / Hydrolase-Antibody complex | |||||||||||||||
Function / homology | ![]() Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / skeletal muscle tissue regeneration / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation ...Dissolution of Fibrin Clot / regulation of hepatocyte proliferation / skeletal muscle tissue regeneration / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / serine-type endopeptidase complex / smooth muscle cell migration / plasminogen activation / positive regulation of smooth muscle cell migration / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / Neutrophil degranulation / positive regulation of reactive oxygen species metabolic process / peptidase activity / regulation of cell population proliferation / angiogenesis / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / positive regulation of cell population proliferation / extracellular space Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Kromann-Hansen, T. / Lange, E.L. / Sorensen, H.P. / Ghassabeh, G.H. / Huang, M. / Jensen, J.K. / Muyldermans, S. / Declerck, P.J. / Andreasen, P.A. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator. Authors: Kromann-Hansen, T. / Louise Lange, E. / Peter Srensen, H. / Hassanzadeh-Ghassabeh, G. / Huang, M. / Jensen, J.K. / Muyldermans, S. / Declerck, P.J. / Komives, E.A. / Andreasen, P.A. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.2 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 894.6 KB | Display | ![]() |
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Full document | ![]() | 902.8 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lhnC ![]() 5lhpC ![]() 5lhrSC ![]() 5lhsC ![]() 4jvpS 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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Components
-Protein / Antibody , 2 types, 2 molecules AB
#1: Protein | Mass: 27554.158 Da / Num. of mol.: 1 / Mutation: C122A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 16303.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 137 molecules ![](data/chem/img/0GJ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-0GJ / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.79 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 100 mM HEPES, 1.6 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40.82 Å / Num. obs: 19919 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 21.91 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.966 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LHR and 4JVP Resolution: 2.6→40.811 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→40.811 Å
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Refine LS restraints |
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LS refinement shell |
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