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Open data
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Basic information
Entry | Database: PDB / ID: 5zae | ||||||
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Title | uPA-6F-HMA | ||||||
![]() | Urokinase-type plasminogen activator chain B | ||||||
![]() | HYDROLASE / Urokinase / Amiloride | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Buckley, B.J. / Jiang, L.G. / Huang, M.D. / Kelso, M.J. / Ranson, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 6-Substituted Hexamethylene Amiloride (HMA) Derivatives as Potent and Selective Inhibitors of the Human Urokinase Plasminogen Activator for Use in Cancer. Authors: Buckley, B.J. / Aboelela, A. / Minaei, E. / Jiang, L.X. / Xu, Z. / Ali, U. / Fildes, K. / Cheung, C.Y. / Cook, S.M. / Johnson, D.C. / Bachovchin, D.A. / Cook, G.M. / Apte, M. / Huang, M. / ...Authors: Buckley, B.J. / Aboelela, A. / Minaei, E. / Jiang, L.X. / Xu, Z. / Ali, U. / Fildes, K. / Cheung, C.Y. / Cook, S.M. / Johnson, D.C. / Bachovchin, D.A. / Cook, G.M. / Apte, M. / Huang, M. / Ranson, M. / Kelso, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.7 KB | Display | ![]() |
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PDB format | ![]() | 48.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5za7C ![]() 5za8C ![]() 5za9C ![]() 5zafC ![]() 5zagC ![]() 5zahC ![]() 5zajC ![]() 5zc5C ![]() 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: 28442.373 Da / Num. of mol.: 1 / Mutation: C122A, N145Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-EAU / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 50mM sodium citrate pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→23.9 Å / Num. obs: 23164 / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.73→1.78 Å / Rmerge(I) obs: 0.686 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DVA Resolution: 1.73→23.9 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.047 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.153 / 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: 26.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→23.9 Å
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Refine LS restraints |
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