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- PDB-6xvd: Crystal structure of complex of urokinase and a upain-1 variant(W... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xvd | |||||||||||||||
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Title | Crystal structure of complex of urokinase and a upain-1 variant(W3F) in pH7.4 condition | |||||||||||||||
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![]() | PEPTIDE BINDING PROTEIN / upain-1-W3F / urokinase / Cyclic peptide inhibitor | |||||||||||||||
Function / homology | ![]() 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 | ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Xue, G.P. / Xie, X. / Zhou, Y. / Yuan, C. / Huang, M.D. / Jiang, L.G. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Insight to the residue in P2 position prevents the peptide inhibitor from being hydrolyzed by serine proteases. Authors: Xue, G. / Xie, X. / Zhou, Y. / Yuan, C. / Huang, M. / Jiang, L. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.9 KB | Display | ![]() |
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PDB format | ![]() | 48.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4dvaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28442.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein/peptide | Mass: 1369.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.05 M sodium citrate at pH 4.5, 1.95 M (NH4)2SO4, 0.05% NaN3, and 5% PEG400 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→60.65 Å / Num. obs: 46337 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.96 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.056 / Num. unique obs: 46337 |
Serial crystallography sample delivery | Method: injection |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4DVA Resolution: 1.4→39.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.993 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 61.06 Å2 / Biso mean: 14.578 Å2 / Biso min: 5.91 Å2
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Refinement step | Cycle: final / Resolution: 1.4→39.83 Å
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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