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- PDB-7e50: Crystal structure of human microplasmin in complex with kazal-typ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7.0E+50 | ||||||
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Title | Crystal structure of human microplasmin in complex with kazal-type inhibitor AaTI | ||||||
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![]() | HYDROLASE / Plasmin | ||||||
Function / homology | ![]() plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Varsha, A.W. / Jobichen, C. / Mok, Y.K. | ||||||
![]() | ![]() Title: Crystal structure of Aedes aegypti trypsin inhibitor in complex with mu-plasmin reveals role for scaffold stability in Kazal-type serine protease inhibitor. Authors: Walvekar, V.A. / Ramesh, K. / Jobichen, C. / Kannan, M. / Sivaraman, J. / Kini, R.M. / Mok, Y.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.2 KB | Display | ![]() |
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PDB format | ![]() | 105.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.1 KB | Display | ![]() |
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Full document | ![]() | 458.3 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d3xS 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: 8820.882 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q1HRB8 | ||||
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#2: Protein | Mass: 27850.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P00747, plasmin | ||||
#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium formate, 20 % polyethylene glycol 3350 pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→44.72 Å / Num. obs: 28769 / % possible obs: 99.6 % / Redundancy: 12.4 % / Rpim(I) all: 0.057 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.85→1.89 Å / Num. unique obs: 1736 / Rpim(I) all: 0.602 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6D3X Resolution: 1.95→19.78 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.1 Å2 / Biso mean: 49.15 Å2 / Biso min: 22.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→19.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: 15.4138 Å / Origin y: 23.1472 Å / Origin z: 11.1548 Å
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Refinement TLS group |
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