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- PDB-6sy3: Cationic Trypsin in Complex with a D-DiPhe-Pro-pyridine derivative -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sy3 | ||||||
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Title | Cationic Trypsin in Complex with a D-DiPhe-Pro-pyridine derivative | ||||||
![]() | 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 | ![]() | 179.4 KB | Display | ![]() |
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PDB format | ![]() | 119.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6hsxC ![]() 6t0mC ![]() 6t0pC ![]() 6t3qC ![]() 6t4aC ![]() 6t5wC ![]() 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
#1: Protein | Mass: 25806.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-LXW / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % |
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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, 25-27% (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: Mar 18, 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: 0.95→43.096 Å / Num. obs: 127390 / % possible obs: 98 % / Redundancy: 4.11 % / Biso Wilson estimate: 8.69 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.043 / Rsym value: 0.038 / Net I/σ(I): 16.04 |
Reflection shell | Resolution: 0.95→1.01 Å / Mean I/σ(I) obs: 1.77 / Num. unique obs: 19451 / CC1/2: 0.74 / Rrim(I) all: 0.58 / Rsym value: 0.49 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MNK Resolution: 0.95→33.8 Å / SU ML: 0.0556 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.6436
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→33.8 Å
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Refine LS restraints |
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LS refinement shell |
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