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- PDB-5yc6: The crystal structure of uPA in complex with 4-Bromobenzylamirne ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yc6 | |||||||||
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Title | The crystal structure of uPA in complex with 4-Bromobenzylamirne at pH4.6 | |||||||||
![]() | Urokinase-type plasminogen activator | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / halogen bonding / serine protease / uPA / P1 group / protease inhibitors / 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 | ![]() ![]() ![]() | |||||||||
![]() | Jiang, L.G. / Zhang, X. / Huang, M.D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases Authors: Jiang, L.G. / Zhang, X. / Zhou, Y. / Chen, Y.Y. / Luo, Z.P. / Li, J.Y. / Yuan, C. / Huang, M.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.6 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.3 KB | Display | ![]() |
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Full document | ![]() | 467.7 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yc7C ![]() 5z1cC ![]() 4dvaS 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
#1: Protein | Mass: 27715.600 Da / Num. of mol.: 1 Fragment: Urokinase-type plasminogen activator chain B, UNP residues 179-324 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Chemical | ChemComp-PZH / | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 50mM sodium citrate (pH 4.6), 2.0M ammonium sulfate supplemented with 5% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→50 Å / Num. obs: 73602 / % possible obs: 97.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 29.5 |
Reflection shell | Highest resolution: 1.13 Å / Rmerge(I) obs: 0.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DVA Resolution: 1.18→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.654 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.049 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.18→50 Å
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Refine LS restraints |
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