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Yorodumi- PDB-1gi5: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gi5 | ||||||
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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: 1.6 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 | 1gi5.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gi5.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gi5_validation.pdf.gz | 700.5 KB | Display | wwPDB validaton report |
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Full document | 1gi5_full_validation.pdf.gz | 702.3 KB | Display | |
Data in XML | 1gi5_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1gi5_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gi5 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gi5 | HTTPS FTP |
-Related structure data
Related structure data | 1ghvC 1ghwC 1ghxC 1ghyC 1ghzC 1gi0C 1gi1C 1gi2C 1gi3C 1gi4C 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 | #4: Chemical | ChemComp-123 / | #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: 2.95 Å3/Da / Density % sol: 58.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.1 Details: magnesium sulfate soak at target pH (10.3). 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: Jun 13, 2000 |
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→69.17 Å / Num. all: 57317 / Num. obs: 32533 / % possible obs: 56.8 % / Observed criterion σ(I): 0.8 / Redundancy: 2.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.46→1.69 Å / Rmerge(I) obs: 0.261 / Num. unique all: 6275 / % possible all: 36.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→7 Å / σ(F): 1.8 / 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, Ser166 Ser170, Ser217, Lys230, Ser236, Ser244 Note that HOH383 ...Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Lys87, Ser110, Ser113, Ser130, Lys159, Ser166 Ser170, Ser217, Lys230, Ser236, Ser244 Note that HOH383 makes short H-bonds to OgSer195 and O6' of the inhibitor Disordered waters are: HOH600 which is close to HOH601, which in turn is close to HOH602; HOH465 which is close to sulfate_466; HOH396 which is close to HOH397; HOH422 which is close to a symmetry-related equivelent of HOH423 HOH654 which occupies the space available when Lys87 is in conformation # 1. HOH674 which is close to HOH675; HOH696 which is close to HOH697; His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonatd.
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Refinement step | Cycle: LAST / Resolution: 1.6→7 Å
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Refine LS restraints |
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