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Yorodumi- PDB-1ghz: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ghz | ||||||
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Title | A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE | ||||||
Components | BETA-TRYPSIN | ||||||
Keywords | HYDROLASE / three-centered / very short hydrogen bond / oxyanion hole water / shift of pKa of His57 / structure-based drug design / specificity / urokinase / trypsin / thrombin / Zn+2-mediated inhibition | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.39 Å | ||||||
Authors | Katz, B.A. / Elrod, K. / Luong, C. / Rice, M. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hatayte, J. / Janc, J. / Link, J. ...Katz, B.A. / Elrod, K. / Luong, C. / Rice, M. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hatayte, J. / Janc, J. / Link, J. / Litvak, J. / Rai, R. / Rice, K. / Sideris, S. / Verner, E. / Young, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. Authors: Katz, B.A. / Elrod, K. / Luong, C. / Rice, M.J. / Mackman, R.L. / Sprengeler, P.A. / Spencer, J. / Hataye, J. / Janc, J. / Link, J. / Litvak, J. / Rai, R. / Rice, K. / Sideris, S. / Verner, E. / Young, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ghz.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ghz.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ghz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ghz_validation.pdf.gz | 667.3 KB | Display | wwPDB validaton report |
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Full document | 1ghz_full_validation.pdf.gz | 670.2 KB | Display | |
Data in XML | 1ghz_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 1ghz_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/1ghz ftp://data.pdbj.org/pub/pdb/validation_reports/gh/1ghz | HTTPS FTP |
-Related structure data
Related structure data | 1ghvC 1ghwC 1ghxC 1ghyC 1gi0C 1gi1C 1gi2C 1gi3C 1gi4C 1gi5C 1gi6C 1gi7C 1gi8C 1gi9C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 287 molecules
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-120 / | #6: 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: 2.04 Å3/Da / Density % sol: 39.73 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.1 Details: magnesium sulfate soak at pH 7.0. vapor diffusion at 298 K, pH 8.10 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8.2 / PH range high: 7.5 | |||||||||||||||||||||||||||||||||||
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: Sep 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→27.47 Å / Num. all: 45834 / Num. obs: 30747 / % possible obs: 67.1 % / Observed criterion σ(I): 0.8 / Redundancy: 2.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.39→1.45 Å / Rmerge(I) obs: 0.285 / Num. unique all: 1510 / % possible all: 31.3 |
Reflection | *PLUS Num. measured all: 74936 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.39→7.5 Å / σ(F): 1.7 / Stereochemistry target values: X-PLOR force field Details: Bulk solvent terms included in Fob file created with standard X-PLOR script. Residues simultaneously refined in two or more conformations are: Gln50, Leu67, Lys87, Met104, Ser110, Lys224, ...Details: Bulk solvent terms included in Fob file created with standard X-PLOR script. Residues simultaneously refined in two or more conformations are: Gln50, Leu67, Lys87, Met104, Ser110, Lys224, Lys230, Ser236. Disordered waters are: HOH324 which is close to a symmetry-related equivalent of HOH327; HOH326 which is close to a symmetry-related equivalent of HOH327; HOH352 which is close to a symmetry-related equivelent of itself; HOH409 which is close to HOH410; HOH425 which is close to HOH426 which in turn is close to HOH427; HOH465 which is close to Sulfate_466; HOH870 which is close to a symmetry-related equivelent of itself; HOH1039 which is close to a symmetry-related equivelent of itself; His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN.
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Refinement step | Cycle: LAST / Resolution: 1.39→7.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 7.5 Å / σ(F): 1.7 / Rfactor all: 0.177 / Rfactor obs: 0.175 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.39 Å / Lowest resolution: 1.45 Å / Rfactor Rfree: 0.211 / Rfactor obs: 0.176 |