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Yorodumi- PDB-6t9v: Bovine Trypsin in complex with the synthetic inhibitor (S)-3-(3-(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t9v | |||||||||
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Title | Bovine Trypsin in complex with the synthetic inhibitor (S)-3-(3-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-2-((3'-fluoro-4'-(hydroxymethyl)-[1,1'-biphenyl])-3-sulfonamido)-3-oxopropyl)benzimidamide (MI-1904) | |||||||||
Components | Cationic Trypsin | |||||||||
Keywords | HYDROLASE / Trypsine / complex / ligand | |||||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12642724334 Å | |||||||||
Authors | Merkl, S. / Keils, A. / Mueller, J.M. / Pilgram, O. / Steinmetzer, T. | |||||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2022 Title: Improving the selectivity of 3-amidinophenylalanine-derived matriptase inhibitors Authors: Pilgram, O. / Keils, A. / Benary, G.E. / Muller, J. / Merkl, S. / Ngaha, S. / Huber, S. / Chevillard, F. / Harbig, A. / Magdolen, V. / Heine, A. / Bottcher-Friebertshauser, E. / Steinmetzer, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t9v.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t9v.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 6t9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/6t9v ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t9v | HTTPS FTP |
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-Related structure data
Related structure data | 6t89C 6t9tC 6t9uC 2zfsS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25806.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 228 molecules
#2: Chemical | ChemComp-TFA / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-MXH / | #6: 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: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 100 mM Imidazole pH 8.0, 100 mM Ammoniumsulfate, 20-25 % PEG8000, 0.1% Sodium-azide, 1 mM Ligand, Protein at 10-20 mg/mL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.12642724334→50 Å / Num. obs: 73657 / % possible obs: 99.2 % / Redundancy: 9.487 % / Biso Wilson estimate: 11.5821453576 Å2 / CC1/2: 0.999 / Rsym value: 0.057 / Net I/σ(I): 18.14 |
Reflection shell | Resolution: 1.13→1.19 Å / Redundancy: 8.81 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 11320 / CC1/2: 0.935 / Rsym value: 0.497 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2zfs Resolution: 1.12642724334→43.9639433495 Å / SU ML: 0.086835831964 / Cross valid method: FREE R-VALUE / σ(F): 1.37586679908 / Phase error: 12.5503789131 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 16.2720204377 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12642724334→43.9639433495 Å
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Refine LS restraints |
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LS refinement shell |
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