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Yorodumi- PDB-6jyp: Crystal structure of uPA_H99Y in complex with 3-azanyl-5-(azepan-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jyp | ||||||
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Title | Crystal structure of uPA_H99Y in complex with 3-azanyl-5-(azepan-1-yl)-N-[bis(azanyl)methylidene]-6-chloranyl-pyrazine-2-carboxamide | ||||||
Components | Urokinase-type plasminogen activatorUrokinase | ||||||
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 / tertiary granule membrane / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / specific granule membrane / regulation of cell adhesion / 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: 2.25 Å | ||||||
Authors | Buckley, B. / Jiang, L.G. / 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 | 6jyp.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jyp.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 6jyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/6jyp ftp://data.pdbj.org/pub/pdb/validation_reports/jy/6jyp | HTTPS FTP |
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-Related structure data
Related structure data | 6ag2C 6ag3C 6ag7C 6ag9C 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: 27740.627 Da / Num. of mol.: 1 / Mutation: H99Y,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-HMX / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 42.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.05M sodium citrate at pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 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: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→60 Å / Num. obs: 10984 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.25→2.29 Å / Rmerge(I) obs: 0.691 / Num. unique obs: 559 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DVA Resolution: 2.25→30.33 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.512 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.255 / 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: 124.16 Å2 / Biso mean: 50.97 Å2 / Biso min: 26.42 Å2
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Refinement step | Cycle: final / Resolution: 2.25→30.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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