+Open data
-Basic information
Entry | Database: PDB / ID: 7vm7 | ||||||
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Title | Crystal structure of inactive uPA in complex with nafamostat | ||||||
Components | Urokinase-type plasminogen activator chain B | ||||||
Keywords | HYDROLASE / uPA / serine protease / nafamostat | ||||||
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 / regulation of signaling receptor activity / negative regulation of plasminogen activation / regulation of smooth muscle cell migration ...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 / regulation of signaling receptor activity / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / 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: 1.87 Å | ||||||
Authors | Jiang, L.G. / Huang, M.D. | ||||||
Funding support | China, 1items
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Citation | Journal: Biophys.J. / Year: 2022 Title: Structural study of the uPA-nafamostat complex reveals a covalent inhibitory mechanism of nafamostat. Authors: Zhou, Y. / Wu, J. / Xue, G. / Li, J. / Jiang, L. / Huang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vm7.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vm7.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vm7_validation.pdf.gz | 633.7 KB | Display | wwPDB validaton report |
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Full document | 7vm7_full_validation.pdf.gz | 636.4 KB | Display | |
Data in XML | 7vm7_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 7vm7_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/7vm7 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/7vm7 | HTTPS FTP |
-Related structure data
Related structure data | 7vm4C 7vm5C 7vm6C 4dvaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27570.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Production host: Komagataella pastoris (fungus) / References: UniProt: P00749 |
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#2: Chemical | ChemComp-7RF / ( |
#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: 2.16 Å3/Da / Density % sol: 42.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2.0 M ammonium sulfate, 5% PEG 400, 20 mM sodium citrate, pH 4.6 |
-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 PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. obs: 19019 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Net I/σ(I): 37.33 |
Reflection shell | Resolution: 1.87→1.94 Å / Rmerge(I) obs: 0.418 / Num. unique obs: 1882 / CC1/2: 0.941 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DVA Resolution: 1.87→39.19 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.566 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→39.19 Å
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