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- PDB-1gi3: A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTER... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gi3 | ||||||
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Title | A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE | ||||||
![]() | BETA-TRYPSIN | ||||||
![]() | 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 | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 87.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 674.2 KB | Display | ![]() |
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Full document | ![]() | 675.3 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ghvC ![]() 1ghwC ![]() 1ghxC ![]() 1ghyC ![]() 1ghzC ![]() 1gi0C ![]() 1gi1C ![]() 1gi2C ![]() 1gi4C ![]() 1gi5C ![]() 1gi6C ![]() 1gi7C ![]() 1gi8C ![]() 1gi9C C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-BMZ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.83 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.1 Details: magnesium sulfate soak at pH 9.52. 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: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 18, 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: 1.32→47.22 Å / Num. all: 65870 / Num. obs: 40323 / % possible obs: 61.2 % / Observed criterion σ(I): 0.8 / Redundancy: 3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.44→1.51 Å / Rmerge(I) obs: 0.255 / Num. unique all: 2334 / % possible all: 37.2 |
Reflection | *PLUS Num. measured all: 110074 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Ser113, Ser130, Lys159, Asp165, Ser170, Ser217, Lys230, Ser236 Note that HOH383 makes short H-bonds to ...Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Ser113, Ser130, Lys159, Asp165, Ser170, Ser217, Lys230, Ser236 Note that HOH383 makes short H-bonds to OgSer195 and O6' of the inhibitor Disordered waters are: HOH304 which is close to HOH305; HOH331 which is close to HOH332; HOH398 which is close to HOH399; HOH407 which is close to HOH408 which is close to HOH409; HOH468 which is close to HOH469 which is close to HOH470; HOH537 which is close to HOH538; HOH618 which is close to HOH619; HOH719 which is close to HOH720 which is close to HOH721; HOH838 which is close to HOH839; HOH917 which is close to HOH918; His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonated.
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Refinement step | Cycle: LAST / Resolution: 1.44→7.5 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7.5 Å / σ(F): 1.8 / % reflection Rfree: 10 % / Rfactor all: 0.206 / Rfactor obs: 0.202 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.44 Å / Lowest resolution: 1.51 Å / Rfactor Rfree: 0.235 / Rfactor obs: 0.206 |