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Yorodumi- PDB-7neu: Inhibitor Complex with Thrombin Activatable Fibrinolysis Inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7neu | ||||||
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Title | Inhibitor Complex with Thrombin Activatable Fibrinolysis Inhibitor (TAFIa) | ||||||
Components | Carboxypeptidase B2 | ||||||
Keywords | HYDROLASE / Inhibitor / complex | ||||||
Function / homology | Function and homology information carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / fibrinolysis / Regulation of Complement cascade / liver regeneration ...carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / fibrinolysis / Regulation of Complement cascade / liver regeneration / cellular response to glucose stimulus / protein catabolic process / blood coagulation / response to xenobiotic stimulus / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å | ||||||
Authors | Brown, D.G. / Schaffner, A.P. / Vuillard, L.M. / Gloanec, P. / Raimbauld, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Phosphinanes and Azaphosphinanes as Potent and Selective Inhibitors of Activated Thrombin-Activatable Fibrinolysis Inhibitor (TAFIa). Authors: Schaffner, A.P. / Sansilvestri-Morel, P. / Despaux, N. / Ruano, E. / Persigand, T. / Rupin, A. / Mennecier, P. / Vallez, M.O. / Raimbaud, E. / Desos, P. / Gloanec, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7neu.cif.gz | 287.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7neu.ent.gz | 236.6 KB | Display | PDB format |
PDBx/mmJSON format | 7neu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7neu_validation.pdf.gz | 858.9 KB | Display | wwPDB validaton report |
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Full document | 7neu_full_validation.pdf.gz | 862.4 KB | Display | |
Data in XML | 7neu_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 7neu_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/7neu ftp://data.pdbj.org/pub/pdb/validation_reports/ne/7neu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 45963.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPB2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q96IY4, carboxypeptidase U |
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#7: Sugar |
-Non-polymers , 6 types, 34 molecules
#2: Chemical | ChemComp-U9K / ( |
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#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-CL / |
#6: Chemical | ChemComp-EDO / |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25 / Details: 100mM MES, 300mM Ammonium Chloride, 35% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→42.06 Å / Num. obs: 12711 / % possible obs: 99.4 % / Redundancy: 4.1 % / CC1/2: 0.01 / Rmerge(I) obs: 0.129 / Net I/σ(I): 14.48 |
Reflection shell | Resolution: 2.8→2.87 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.32 / Num. unique obs: 1240 / CC1/2: 0.001 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→42.02 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.821 / SU B: 38.84 / SU ML: 0.352 / Cross valid method: FREE R-VALUE / ESU R Free: 0.419 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.706 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→42.02 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -27.3585 Å / Origin y: -20.5237 Å / Origin z: 8.1501 Å
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Refinement TLS group |
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