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Yorodumi- PDB-6ag3: Crystal structure of uPA in complex with 3,5-bis(azanyl)-N-carbam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ag3 | ||||||
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Title | Crystal structure of uPA in complex with 3,5-bis(azanyl)-N-carbamimidoyl-6-(2,4-dimethoxypyrimidin-5-yl)pyrazine-2-carboxamide | ||||||
Components | Urokinase-type plasminogen activator | ||||||
Keywords | HYDROLASE / Urokinase / Amiloride | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Buckley, B. / Jiang, L.G. / Majed, H. / Huang, M.D. / Kelso, M. / Ranson, M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: uPA-HMA Authors: Buckley, B. / Jiang, L.G. / Huang, M.D. / Kelso, M. / Ranson, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ag3.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ag3.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ag3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ag3_validation.pdf.gz | 746.6 KB | Display | wwPDB validaton report |
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Full document | 6ag3_full_validation.pdf.gz | 750.6 KB | Display | |
Data in XML | 6ag3_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 6ag3_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/6ag3 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/6ag3 | HTTPS FTP |
-Related structure data
Related structure data | 6ag2C 6ag7C 6ag9C 6jypC 4dvaS S: Starting model for refinement C: citing same article (ref.) |
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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: C122A, N145Q 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: Chemical | ChemComp-9XC / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % |
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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% polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→60.45 Å / Num. obs: 8040 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.558 / Num. unique obs: 396 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DVA Resolution: 2.48→60.45 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.503 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R Free: 0.344 / 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 max: 106.75 Å2 / Biso mean: 47.81 Å2 / Biso min: 25.65 Å2
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Refinement step | Cycle: final / Resolution: 2.48→60.45 Å
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