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- PDB-5xw9: Crystal Structure of Porcine pancreatic trypsin with tripeptide i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xw9 | ||||||
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Title | Crystal Structure of Porcine pancreatic trypsin with tripeptide inhibitor, PRY, at pH 7 | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / protease / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saikhedkar, N.S. / Bhoite, A.S. / Giri, A.P. / Kulkarni, K.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Tripeptides derived from reactive centre loop of potato type II protease inhibitors preferentially inhibit midgut proteases of Helicoverpa armigera. Authors: Saikhedkar, N.S. / Joshi, R.S. / Bhoite, A.S. / Mohandasan, R. / Yadav, A.K. / Fernandes, M. / Kulkarni, K.A. / Giri, A.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 75.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.4 KB | Display | ![]() |
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Full document | ![]() | 432.6 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xw8C ![]() 5xwaC ![]() 5xwjC ![]() 5xwlC ![]() 4doqS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 14238.919 Da / Num. of mol.: 1 / Fragment: UNP residues 1-133 / Source method: isolated from a natural source Details: Commercially available trypsin from Sigma (Cat. no. T4799) Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 10207.492 Da / Num. of mol.: 1 / Fragment: UNP residues 134-231 / Source method: isolated from a natural source Details: Commercially available trypsin from Sigma (Cat. no. T4799) Source: (natural) ![]() ![]() |
#3: Protein/peptide | Mass: 461.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Compound details | There is autolysis of Trypsin at residue 133, thus Trypsin is split into two entities. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 70% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→71.5 Å / Num. obs: 19062 / % possible obs: 100 % / Redundancy: 16.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1872 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DOQ Resolution: 2→63.214 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.7 / 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: 2→63.214 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -7.8267 Å / Origin y: 33.1091 Å / Origin z: -6.3854 Å
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Refinement TLS group | Selection details: (chain A and resseq 9:132) or (chain B and resseq 134-231) |