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Yorodumi- PDB-1gj6: ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER19... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gj6 | ||||||
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Title | ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER190 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS | ||||||
Components | BETA-TRYPSIN | ||||||
Keywords | HYDROLASE / selectivity at S1 / H2O displacement / uPA / tPA / Ser190/Ala190 protease / structure-based drug design | ||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Katz, B.A. / Sprengeler, P.A. / Luong, C. / Verner, E. / Spencer, J.R. / Breitenbucher, J.G. / Hui, H. / McGee, D. / Allen, D. / Martelli, A. / Mackman, R.L. | ||||||
Citation | Journal: Chem.Biol. / Year: 2001 Title: Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets. Authors: Katz, B.A. / Sprengeler, P.A. / Luong, C. / Verner, E. / Elrod, K. / Kirtley, M. / Janc, J. / Spencer, J.R. / Breitenbucher, J.G. / Hui, H. / McGee, D. / Allen, D. / Martelli, A. / Mackman, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gj6.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gj6.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gj6_validation.pdf.gz | 691.9 KB | Display | wwPDB validaton report |
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Full document | 1gj6_full_validation.pdf.gz | 692.4 KB | Display | |
Data in XML | 1gj6_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1gj6_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/1gj6 ftp://data.pdbj.org/pub/pdb/validation_reports/gj/1gj6 | HTTPS FTP |
-Related structure data
Related structure data | 1gj4C 1gj5C 1gj7C 1gj8C 1gj9C 1gjaC 1gjbC 1gjcC 1gjdC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-132 / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.1 Details: magnesium sulfate soak at pH 9.05, vapor diffusion at 298 K, pH 8.10 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: batch method / Details: Katz, B.A., (2000) Chem.Biol., 7, 299. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 16, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→46.97 Å / Num. all: 58194 / Num. obs: 32043 / % possible obs: 55.1 % / Observed criterion σ(I): 0.8 / Redundancy: 2.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.55→1.57 Å / Rmerge(I) obs: 0.266 / Num. unique all: 664 / % possible all: 37.1 |
Reflection | *PLUS Num. obs: 30523 / Rmerge(I) obs: 0.083 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→7 Å / σ(F): 1.6 / Stereochemistry target values: X-PLOR force field Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Ser110, Ser113, Ser130, Lys159, Asp165, Ser170, Gln175, Ser217, Lys230, Ser236, Ser244 Note that ...Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Ser110, Ser113, Ser130, Lys159, Asp165, Ser170, Gln175, Ser217, Lys230, Ser236, Ser244 Note that HOH383 makes short H-bonds to OgSer195 and O6' of the inhibitor Disordered waters are: HOH249 which is close to HOH250; HOH372 which is close to HOH373; HOH397 which is close to HOH398; HOH399 which is close to HOH400; sulfate_458 which is close to HOH459; HOH536 which is close to HOH537; HOH647 which is close to HOH648; HOH667 which is close to HOH668; HOH679 which is close to HOH680; HOH684 which is close to HOH685; HOH797 which is close to HOH798 which is close to HOH799; HOH902 which is close to HOH903; HOH947 which is close to HOH948; His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonated.
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Refinement step | Cycle: LAST / Resolution: 1.5→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / % reflection Rfree: 10 % / Rfactor all: 0.189 / Rfactor obs: 0.15 / Rfactor Rwork: 0.15 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å / Rfactor Rwork: 0.189 / Rfactor obs: 0.189 |