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- PDB-4zkr: The crystal structure of upain-1-W3A in complex with uPA at pH9.0 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zkr | ||||||
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Title | The crystal structure of upain-1-W3A in complex with uPA at pH9.0 | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / Peptides inhibitor / uPA / serine protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Jiang, L. / Andreasen, P.A. / Huang, M. | ||||||
![]() | ![]() Title: The crystal structure of mupain-1-IG in complex with murinised human uPA at pH7.4 Authors: Jiang, L. / Andreasen, P.A. / Huang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4zknC ![]() 4zkoC ![]() 4zksC ![]() 4dvaS S: Starting model for refinement C: citing same article ( |
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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: 27844.715 Da / Num. of mol.: 1 / Fragment: UNP residues 179-425 / Mutation: C122A, N145Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein/peptide | Mass: 1379.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-P6G / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 50 mM sodium citrate pH 4.6, 2.0 M ammonium sulfate supplemented with 5% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HS / Detector: CCD / Date: Oct 23, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→50 Å / Num. obs: 46198 / % possible obs: 91.3 % / Redundancy: 4.9 % / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.36→1.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 1.7 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DVA Resolution: 1.36→24.11 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 0.979 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.074 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→24.11 Å
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