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Open data
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Basic information
Entry | Database: PDB / ID: 5za7 | ||||||
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Title | uPA-HMA | ||||||
![]() | Urokinase-type plasminogen activator chain B | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 66 KB | Display | ![]() |
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PDB format | ![]() | 46.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5za8C ![]() 5za9C ![]() 5zaeC ![]() 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-HMX / |
#3: Chemical | ChemComp-SO4 / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.36 % |
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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 PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→50 Å / Num. obs: 24670 / % possible obs: 97.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.691 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4DVA Resolution: 1.7→34.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.678 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.8 Å
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Refine LS restraints |
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