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Yorodumi- PDB-1gi0: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gi0 | ||||||
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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: 1.42 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 | 1gi0.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gi0.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gi0_validation.pdf.gz | 682.3 KB | Display | wwPDB validaton report |
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Full document | 1gi0_full_validation.pdf.gz | 685.3 KB | Display | |
Data in XML | 1gi0_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 1gi0_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gi0 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gi0 | HTTPS FTP |
-Related structure data
Related structure data | 1ghvC 1ghwC 1ghxC 1ghyC 1ghzC 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, 269 molecules
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-BMZ / | #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: 2.03 Å3/Da / Density % sol: 39.49 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.1 Details: magnesium sulfate soak at pH 3.50. 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 5, 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→27.43 Å / Num. all: 45969 / Num. obs: 28657 / % possible obs: 62.2 % / Observed criterion σ(I): 0.8 / Redundancy: 2.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.42→1.48 Å / Rmerge(I) obs: 0.302 / Num. unique all: 1696 / % possible all: 37.8 |
Reflection | *PLUS Num. measured all: 69879 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.42→7 Å / σ(F): 1.85 / Stereochemistry target values: X-PLOR force field Details: Residues simultaneously refined in two or more conformations are: Thr26, Val31, Ser49, Gln50, Val53, Leu67, Met104, Ser110, Ser116, Lys224, Ser236. Note that HOH383 makes short H-bonds to ...Details: Residues simultaneously refined in two or more conformations are: Thr26, Val31, Ser49, Gln50, Val53, Leu67, Met104, Ser110, Ser116, Lys224, Ser236. Note that HOH383 makes short H-bonds to OgSer195 and O6' of the inhibitor Disordered waters are: HOH292 which is close to HOH293; HOH344 which is close to HOH345; HOH357 which is close to HOH358; HOH410 which is close to HOH411; HOH493 which is close to a symmetry-related equivalent of HOH494; HOH911 which is close to HOH912; HOH1010 which is close to HOH1011; HOH1012 which is close to a symmetry-related equivalent of itself; HIS91 is MONOPROTONATED ON THE EPSILON NITROGEN. His40 and His57 are doubly protonatd.
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Refinement step | Cycle: LAST / Resolution: 1.42→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): 1.85 / Rfactor all: 0.181 / Rfactor obs: 0.179 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.42 Å / Lowest resolution: 1.48 Å / Rfactor Rfree: 0.219 / Rfactor obs: 0.183 |