+Open data
-Basic information
Entry | Database: PDB / ID: 5wxf | ||||||
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Title | Crystal structure of uPA in complex with upain-2-2 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Serine proteases / uPA / pepetide inhibitors / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) Phage display vector pTDisp (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Jiang, L. / Huang, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochim. Biophys. Acta / Year: 2018 Title: Cleavage of peptidic inhibitors by target protease is caused by peptide conformational transition. Authors: Jiang, L. / Oldenburg, E. / Kromann-Hansen, T. / Xu, P. / Jensen, J.K. / Andreasen, P.A. / Huang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wxf.cif.gz | 122.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wxf.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 5wxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/5wxf ftp://data.pdbj.org/pub/pdb/validation_reports/wx/5wxf | HTTPS FTP |
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-Related structure data
Related structure data | 5wxoC 5wxpC 2nwnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28442.373 Da / Num. of mol.: 1 / Mutation: C299A/N322Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Komagataella pastoris (fungus) / References: UniProt: P00749, u-plasminogen activator |
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#2: Protein/peptide | Mass: 1361.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Phage display vector pTDisp (others) |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 50 mM sodium citrate, pH 4.6, and 2.0 M ammonium sulfate supplemented with 5% polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→57.57 Å / Num. obs: 35325 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 36.4 |
Reflection shell | Rmerge(I) obs: 0.244 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NWN Resolution: 1.46→57.57 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.47 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.094 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.46→57.57 Å
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Refine LS restraints |
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