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- PDB-1o38: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Bindin... -
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Basic information
Entry | Database: PDB / ID: 1o38 | ||||||
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Title | Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors | ||||||
![]() | BETA-TRYPSIN | ||||||
![]() | HYDROLASE / serine protease / short hydrogen bond / inhibition mechanism / shift of pKa / trypsin / thrombin / urokinase / factor Xa | ||||||
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. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. ...Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W. | ||||||
![]() | ![]() Title: Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors. Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W. / Hui, H.C. / Breitenbucher, J.G. ...Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.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 | ![]() | 112.4 KB | Display | ![]() |
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PDB format | ![]() | 88.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 720.1 KB | Display | ![]() |
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Full document | ![]() | 723.6 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o2gC ![]() 1o2hC ![]() 1o2iC ![]() 1o2jC ![]() 1o2kC ![]() 1o2lC ![]() 1o2mC ![]() 1o2nC ![]() 1o2oC ![]() 1o2pC ![]() 1o2qC ![]() 1o2rC ![]() 1o2sC ![]() 1o2tC ![]() 1o2uC ![]() 1o2vC ![]() 1o2wC ![]() 1o2xC ![]() 1o2yC ![]() 1o2zC ![]() 1o30C ![]() 1o31C ![]() 1o32C ![]() 1o33C ![]() 1o34C ![]() 1o35C ![]() 1o36C ![]() 1o37C ![]() 1o39C ![]() 1o3aC ![]() 1o3bC ![]() 1o3cC ![]() 1o3dC ![]() 1o3eC ![]() 1o3fC ![]() 1o3gC ![]() 1o3hC ![]() 1o3iC ![]() 1o3jC ![]() 1o3kC ![]() 1o3lC ![]() 1o3mC ![]() 1o3nC ![]() 1o3oC ![]() 1o3pC 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-SO4 / |
#4: Chemical | ChemComp-653 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.1 Details: magnesium sulfate soak at target pH (7.50). vapor diffusion at 298 K, pH 8.10 |
-Data collection
Diffraction | Mean temperature: 285 K / Ambient temp details: Crystal Cooler |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 15, 2002 |
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→21.98 Å / Num. all: 57756 / Num. obs: 53257 / % possible obs: 92.2 % / Observed criterion σ(F): 0.55 / Redundancy: 4.4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.38→1.44 Å / % possible obs: 41.4 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 1.3 / Num. unique all: 7173 / % possible all: 43.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Residues simultaneously refined in two or more conformations are: Ser37, Val53, Leu66, Ser86, Ser110, Se113, Ser130, Lys159, Asp165, Ser170, Gln175, Ser195, Ser217, Lys230, Ser236. Note that ...Details: Residues simultaneously refined in two or more conformations are: Ser37, Val53, Leu66, Ser86, Ser110, Se113, Ser130, Lys159, Asp165, Ser170, Gln175, Ser195, Ser217, Lys230, Ser236. Note that HOH383 makes short H-bonds with OgSer195 (ALT1) and O6' of the inhibitor Disordered water: HOH944 (ALT2) is close to Asp165 (ALT1). His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonated.
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Refinement step | Cycle: LAST / Resolution: 1.38→7 Å
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Refine LS restraints |
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