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- PDB-6u22: Crystal structure of SFTI-triazole inhibitor in complex with beta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6u22 | ||||||
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Title | Crystal structure of SFTI-triazole inhibitor in complex with beta-trypsin | ||||||
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![]() | HYDROLASE/INHIBITOR / Triazole / Peptidomimetic / BIOSYNTHETIC PROTEIN / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() negative regulation of endopeptidase activity / endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / protease binding / serine-type endopeptidase activity ...negative regulation of endopeptidase activity / endopeptidase inhibitor activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / protease binding / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | White, A.M. / King, G.J. / Durek, T. / Craik, D.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Application and Structural Analysis of Triazole-Bridged Disulfide Mimetics in Cyclic Peptides. Authors: White, A.M. / de Veer, S.J. / Wu, G. / Harvey, P.J. / Yap, K. / King, G.J. / Swedberg, J.E. / Wang, C.K. / Law, R.H.P. / Durek, T. / Craik, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143 KB | Display | ![]() |
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PDB format | ![]() | 110.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 306.3 KB | Display | ![]() |
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Full document | ![]() | 306.3 KB | Display | |
Data in XML | ![]() | 1.3 KB | Display | |
Data in CIF | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6q1uC ![]() 6u24C ![]() 6u7qC ![]() 6u7rC ![]() 6u7sC ![]() 6u7uC ![]() 6u7wC ![]() 6u7xC ![]() 6vxyC ![]() 6vy8C ![]() 1sfiS 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: Protein/peptide | Mass: 1471.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-WMH / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Precipitant: PEG4000 (25%-35% w/v), TrisBase (0.1 M, 8.5-9.5 pH) and NH4Ac (0.26 M). Protein solution: 22 mg/mL in Tris.HCl (0.1 M, pH 8.0) with CaCl2 (10 mM) PH range: 8.5-9.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→46.85 Å / Num. obs: 52571 / % possible obs: 99.5 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.42→1.44 Å / Rmerge(I) obs: 0.371 / Num. unique obs: 2321 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SFI Resolution: 1.42→37.462 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 15.46 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.15 Å2 / Biso mean: 21.3542 Å2 / Biso min: 10.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.42→37.462 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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