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- PDB-6t5w: Cationic Trypsin in Complex with a D-Phe-Pro-p-aminopyridine Deri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t5w | ||||||
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Title | Cationic Trypsin in Complex with a D-Phe-Pro-p-aminopyridine Derivative (cocrystallizaton at 291 K) | ||||||
![]() | Cationic Trypsin | ||||||
![]() | HYDROLASE / PROTEASE / SERINE PROTEASE / DIGESTION / METAL ION BINDING | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ngo, K. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins? Authors: Ngo, K. / Collins-Kautz, C. / Gerstenecker, S. / Wagner, B. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.8 KB | Display | ![]() |
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PDB format | ![]() | 113.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 959.3 KB | Display | ![]() |
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Full document | ![]() | 959.2 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hsxC ![]() 6sy3C ![]() 6t0mC ![]() 6t0pC ![]() 6t3qC ![]() 6t4aC ![]() 6tdtC ![]() 5mnkS 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
-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) ![]() ![]() |
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-Non-polymers , 5 types, 205 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/J5K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/J5K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-J5K / ( |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M (NH4)2SO4, 0.1 M imidazole, 0.1% (w/v) sodium azide, 25% (w/v) PEG8000 PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.128→43.115 Å / Num. obs: 76852 / % possible obs: 99.5 % / Redundancy: 5 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.058 / Rsym value: 0.052 / Net I/σ(I): 14.55 |
Reflection shell | Resolution: 1.13→1.2 Å / Mean I/σ(I) obs: 2.55 / Num. unique obs: 12065 / CC1/2: 0.836 / Rrim(I) all: 0.539 / Rsym value: 0.48 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MNK Resolution: 1.13→43.11 Å / SU ML: 0.0792 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 11.934 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: 14.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→43.11 Å
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Refine LS restraints |
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LS refinement shell |
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