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Yorodumi- PDB-6d3y: Highly Potent and Selective Plasmin Inhibitors Based on the Sunfl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d3y | ||||||
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Title | Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma | ||||||
Components |
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Keywords | HYDROLASE / proteases / SFTI / complex / fibrinolysis | ||||||
Function / homology | Function and homology information 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 / negative regulation of endopeptidase activity ...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 / negative regulation of endopeptidase activity / 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 / endopeptidase inhibitor activity / 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 / serine-type endopeptidase inhibitor activity / 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 / protease binding / collagen-containing extracellular matrix / 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 | Homo sapiens (human) Helianthus annuus (common sunflower) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 Å | ||||||
Authors | Law, R.H.P. / Wu, G. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2019 Title: Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma. Authors: Swedberg, J.E. / Wu, G. / Mahatmanto, T. / Durek, T. / Caradoc-Davies, T.T. / Whisstock, J.C. / Law, R.H.P. / Craik, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d3y.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d3y.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 6d3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/6d3y ftp://data.pdbj.org/pub/pdb/validation_reports/d3/6d3y | HTTPS FTP |
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-Related structure data
Related structure data | 6d3xC 6d3zC 6d40C 1sfiS 5uggS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27096.135 Da / Num. of mol.: 1 / Fragment: UNP residues 564-810 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Komagataella pastoris (fungus) / References: UniProt: P00747, plasmin | ||
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#2: Protein/peptide | Mass: 1579.865 Da / Num. of mol.: 1 / Fragment: UNP residues 40-53 / Mutation: I7R / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5 | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M 2-ethanesulfonic acid, 0.15 M ammonium sulfate, 13% PEG4000 PH range: 5-7 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.32→74.903 Å / Num. obs: 60637 / % possible obs: 97.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 10.42 Å2 / Rpim(I) all: 0.056 / Rrim(I) all: 0.115 / Rsym value: 0.1 / Net I/av σ(I): 4.1 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 5UGG & 1SFI Resolution: 1.32→40.455 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.23 Å2 / Biso mean: 17.459 Å2 / Biso min: 5.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.32→40.455 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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