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- PDB-5mnn: Cationic trypsin in complex with N-amidinopiperidine (deuterated ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mnn | ||||||
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Title | Cationic trypsin in complex with N-amidinopiperidine (deuterated sample at 100 K) | ||||||
![]() | Cationic trypsin | ||||||
![]() | HYDROLASE / hydrogen bonding / protonation / protein-ligand interaction | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Schiebel, J. / Heine, A. / Klebe, G. | ||||||
Funding support | 1items
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![]() | ![]() Title: Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes. Authors: Schiebel, J. / Gaspari, R. / Wulsdorf, T. / Ngo, K. / Sohn, C. / Schrader, T.E. / Cavalli, A. / Ostermann, A. / 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 | ![]() | 147.4 KB | Display | ![]() |
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PDB format | ![]() | 117 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.9 KB | Display | ![]() |
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Full document | ![]() | 433.7 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mneC ![]() 5mnfC ![]() 5mngC ![]() 5mnhC ![]() 5mnoC ![]() 5mnqC ![]() 5mnzC ![]() 5mo0C ![]() 5mo2C ![]() 5mopC ![]() 5moqC ![]() 5mosC ![]() 4i8hS 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: 23324.287 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-MRZ / | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 17.5% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7069 Å / Relative weight: 1 |
Reflection | Resolution: 0.859→42.325 Å / Num. obs: 179705 / % possible obs: 99.1 % / Redundancy: 8.538 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 27.35 |
Reflection shell | Resolution: 0.859→0.91 Å / Redundancy: 8.438 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3.56 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I8H Resolution: 0.859→39.858 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 7.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.859→39.858 Å
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Refine LS restraints |
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LS refinement shell |
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