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Open data
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Basic information
Entry | Database: PDB / ID: 1ce5 | ||||||
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Title | BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZAMIDINE | ||||||
![]() | PROTEIN (TRYPSIN) | ||||||
![]() | HYDROLASE / HYDROLASE (SERINE PROTEINASE) | ||||||
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 | ![]() ![]() | ||||||
![]() | Ota, N. / Stroupe, C. / Ferreira-Da-Silva, J.M.S. / Shah, S.S. / Mares-Guia, M. / Brunger, A.T. | ||||||
![]() | ![]() Title: Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine. Authors: Ota, N. / Stroupe, C. / Ferreira-da-Silva, J.M. / Shah, S.A. / Mares-Guia, M. / Brunger, A.T. #1: ![]() Title: Crystal structure of bovine beta-trypsin at 1.5 A resolution in a crystal form with low molecular packing density. Active site geometry, ion pairs and solvent structure. Authors: Bartunik, H.D. / Summers, L.J. / Bartsch, H.H. #2: ![]() Title: The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors Authors: Marquart, M. / Walter, J. / Deisenhofer, J. / Bode, W. / Huber, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.1 KB | Display | ![]() |
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PDB format | ![]() | 40.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.3 KB | Display | ![]() |
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Full document | ![]() | 454.8 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bzaC ![]() 3ptbS S: Starting model for refinement 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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Unit cell |
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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 Details: BOVINE PANCREAS BETA-TRYPSIN PURCHASED FROM WORTHINGTON BIOCHEMICAL CORPORATION Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 131 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-BEN / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.92 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24 Å / Num. obs: 21208 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.07 / Net I/σ(I): 19.25 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.96 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.201 / % possible all: 84 |
Reflection | *PLUS Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 84 % / Rmerge(I) obs: 0.201 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3PTB Resolution: 1.9→24 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 310285.4 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.1 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 24 Å / σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.213 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.184 / Num. reflection obs: 1881 |