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Yorodumi- PDB-1gi4: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gi4 | ||||||
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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 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: 1.37 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 | 1gi4.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gi4.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gi4_validation.pdf.gz | 722.3 KB | Display | wwPDB validaton report |
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Full document | 1gi4_full_validation.pdf.gz | 725 KB | Display | |
Data in XML | 1gi4_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1gi4_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gi4 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gi4 | HTTPS FTP |
-Related structure data
Related structure data | 1ghvC 1ghwC 1ghxC 1ghyC 1ghzC 1gi0C 1gi1C 1gi2C 1gi3C 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
-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, 279 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-122 / |
#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: 2.97 Å3/Da / Density % sol: 58.56 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.1 Details: magnesium sulfate soak at target pH. 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 13, 1997 |
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→37.58 Å / Num. all: 65909 / Num. obs: 49930 / % possible obs: 75.8 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.37→1.43 Å / Rmerge(I) obs: 0.248 / Num. unique all: 2480 / % possible all: 34.3 |
Reflection | *PLUS Num. measured all: 191096 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.37→7 Å / σ(F): 1.8 / 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: Val53, Leu66, Ser86, Lys87, Leu99, Ser113, ...Details: Bulk solvent terms included in Fob file created with standard X-PLOR script. Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Leu99, Ser113, Ser130, Gln135, Asp165, Ser166, Ser170, Gln175, Ser217, Lys230, Ser236 Disordered waters are: HOH271 which is close to HOH272; HOH349 which is close to HOH350; HOH756 which is close to Lys230 in conformation 1, but makes an H-bond to Lys230 in conformation 2. His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonatd.
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Refinement step | Cycle: LAST / Resolution: 1.37→7 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 Å / σ(F): 1.8 / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.37 Å / Lowest resolution: 1.43 Å / Rfactor Rfree: 0.214 / Rfactor obs: 0.193 |