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- PDB-5mnx: Neutron structure of cationic trypsin in complex with 2-aminopyridine -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mnx | |||||||||
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Title | Neutron structure of cationic trypsin in complex with 2-aminopyridine | |||||||||
![]() | 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 | NEUTRON DIFFRACTION / NUCLEAR REACTOR / ![]() | |||||||||
![]() | Schiebel, J. / Schrader, T.E. / Ostermann, A. / Heine, A. / Klebe, G. | |||||||||
Funding support | 1items
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![]() | ![]() Title: Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin. Authors: Schiebel, J. / Gaspari, R. / Sandner, A. / Ngo, K. / Gerber, H.D. / 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 | ![]() | 100.2 KB | Display | ![]() |
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PDB format | ![]() | 76.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 336 KB | Display | ![]() |
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Full document | ![]() | 336 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mn1C ![]() 5mnaC ![]() 5mnbC ![]() 5mncC ![]() 5mnyC ![]() 5monC ![]() 5mooC ![]() 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-2AP / |
#4: Chemical | ChemComp-DOD / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
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, 16% (w/v) PEG 8000 |
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: NUCLEAR REACTOR / Site: FRM II ![]() |
Detector | Type: MAATEL BIODIFF / Detector: IMAGE PLATE / Date: Jul 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron |
Radiation wavelength | Wavelength: 2.675 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→25 Å / Num. obs: 38142 / % possible obs: 90.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.493 |
Reflection shell | Resolution: 1.42→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.051 / % possible all: 69.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I8H Resolution: 1.42→22.166 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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