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Yorodumi- PDB-1gi2: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gi2 | ||||||
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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: 1.38 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 | 1gi2.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gi2.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gi2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gi2 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gi2 | HTTPS FTP |
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-Related structure data
Related structure data | 1ghvC 1ghwC 1ghxC 1ghyC 1ghzC 1gi0C 1gi1C 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
#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-SO4 / |
#4: Chemical | ChemComp-122 / |
#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: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.1 Details: magnesium sulfate soak at target pH (8.1). vapor diffusion at 298 K, pH 8.10 |
-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: Jul 25, 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→67.43 Å / Num. all: 51781 / Num. obs: 36102 / % possible obs: 69.7 % / Observed criterion σ(I): 0.8 / Redundancy: 2.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.38→1.44 Å / Rmerge(I) obs: 0.275 / Num. unique all: 1889 / % possible all: 34.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.38→7 Å / σ(F): 1.7 / Stereochemistry target values: X-PLOR force field Details: Residues simultaneously refined in two or more conformations are: Val53, Ser61, Ser84, Ser86, Leu99, Met104, Ser113, Ser116, Arg117, Ser127 Gln135, Ser146, Asp165, Ser166, Ser167, Gln175, ...Details: Residues simultaneously refined in two or more conformations are: Val53, Ser61, Ser84, Ser86, Leu99, Met104, Ser113, Ser116, Arg117, Ser127 Gln135, Ser146, Asp165, Ser166, Ser167, Gln175, Ser217, Ser236, Ser244. Note that HOH383 makes short H-bonds to OgSer195 and O6' of the inhibitor Disordered waters are: HOH379 which is close to sulfate_380; HOH425 which is close to HOH426; HOH461 which is close to a symmetry-related equivalent of HOH462; HOH604 which is close to HOH605; HIS91 is MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonatd.
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Refinement step | Cycle: LAST / Resolution: 1.38→7 Å
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Refine LS restraints |
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