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Yorodumi- PDB-1nc6: Potent, small molecule inhibitors of human mast cell tryptase. An... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nc6 | ||||||
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Title | Potent, small molecule inhibitors of human mast cell tryptase. Anti-asthmatic action of a dipeptide-based transition state analogue containing benzothiazole ketone | ||||||
Components | Trypsinogen | ||||||
Keywords | HYDROLASE / protein-inhibitor complex | ||||||
Function / homology | Function and homology information cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Costanzo, M.J. / Yabut, S.C. / Almond Jr., H.R. / Andrade-Gordon, P. / Corcoran, T.W. / de Garavilla, L. / Kauffman, J.A. / Abraham, W.M. / Recacha, R. / Chattopadhyay, D. / Maryanoff, B.E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2003 Title: Potent, Small-Molecule Inhibitors of Human Mast Cell Tryptase. Antiasthmatic Action of a Dipeptide-Based Transition-State Analogue Containing a Benzothiazole Ketone. Authors: Costanzo, M.J. / Yabut, S.C. / Almond Jr., H.R. / Andrade-Gordon, P. / Corcoran, T.W. / De Garavilla, L. / Kauffman, J.A. / Abraham, W.M. / Recacha, R. / Chattopadhyay, D. / Maryanoff, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nc6.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nc6.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nc6_validation.pdf.gz | 787.5 KB | Display | wwPDB validaton report |
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Full document | 1nc6_full_validation.pdf.gz | 791 KB | Display | |
Data in XML | 1nc6_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1nc6_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/1nc6 ftp://data.pdbj.org/pub/pdb/validation_reports/nc/1nc6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-ABB / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.76 Å3/Da / Density % sol: 29.55 % | |||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: magnesium chloride, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2000 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→99 Å / Num. all: 15217 / Num. obs: 15384 / % possible obs: 98.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 10.5 Å2 |
Reflection shell | Resolution: 1.9→2.02 Å / % possible all: 97.6 |
Reflection | *PLUS Highest resolution: 1.9 Å / % possible obs: 98.6 % / Rmerge(I) obs: 0.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→17.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1231211.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.6246 Å2 / ksol: 0.419788 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→17.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |