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Yorodumi- PDB-4x1n: The crystal structure of mupain-1-16 in complex with murinised hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x1n | |||||||||||||||||||||
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Title | The crystal structure of mupain-1-16 in complex with murinised human uPA at pH7.4 | |||||||||||||||||||||
Components |
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Keywords | HYDROLASE INHIBITOR/HYDROLASE / Serine protease / peptidic inhibitor / uPA / HYDROLASE INHIBITOR-HYDROLASE 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 / 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) synthetic construct (others) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||||||||||||||
Authors | Jiang, L. / Zhao, B. / Xu, P. / Andreasen, P. / Huang, M. | |||||||||||||||||||||
Funding support | China, Denmark, 6items
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Citation | Journal: Plos One / Year: 2014 Title: A cyclic peptidic serine protease inhibitor: increasing affinity by increasing peptide flexibility. Authors: Zhao, B. / Xu, P. / Jiang, L. / Paaske, B. / Kromann-Hansen, T. / Jensen, J.K. / Srensen, H.P. / Liu, Z. / Nielsen, J.T. / Christensen, A. / Hosseini, M. / Srensen, K.K. / Nielsen, N.C. / ...Authors: Zhao, B. / Xu, P. / Jiang, L. / Paaske, B. / Kromann-Hansen, T. / Jensen, J.K. / Srensen, H.P. / Liu, Z. / Nielsen, J.T. / Christensen, A. / Hosseini, M. / Srensen, K.K. / Nielsen, N.C. / Jensen, K.J. / Huang, M. / Andreasen, P.A. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x1n.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x1n.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 4x1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/4x1n ftp://data.pdbj.org/pub/pdb/validation_reports/x1/4x1n | HTTPS FTP |
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-Related structure data
Related structure data | 4x1qC 4x1rC 4x1sC 2nwnS 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/peptide | Mass: 1105.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Protein | Mass: 27869.742 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 179-425 / Mutation: C299A, H272Y, 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 |
#3: Chemical | ChemComp-MRZ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2.0M ammonium sulfate, 50mM sodium citrate pH 4.6, 5% PEG 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 315 / Detector: CCD / Date: May 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 21312 / % possible obs: 98.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NWN Resolution: 1.8→35.13 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.402 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.164 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.13 Å
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Refine LS restraints |
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