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- PDB-3fp7: Anionic trypsin variant S195A in complex with bovine pancreatic t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fp7 | ||||||
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Title | Anionic trypsin variant S195A in complex with bovine pancreatic trypsin inhibitor (BPTI) cleaved at the scissile bond (LYS15-ALA16) determined to the 1.46 A resolution limit | ||||||
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![]() | Hydrolase/Hydrolase inhibitor / ENZYME-INHIBITOR COMPLEX / PEPTIDE BOND HYDROLYSIS / Calcium / Digestion / Hydrolase / Metal-binding / Protease / Secreted / Serine protease / Zymogen / Pharmaceutical / Protease inhibitor / Serine protease inhibitor / Hydrolase-Hydrolase inhibitor COMPLEX | ||||||
Function / homology | ![]() Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / Neutrophil degranulation ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / Neutrophil degranulation / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / collagen catabolic process / trypsin / serine protease inhibitor complex / digestion / response to nutrient / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zakharova, E. / Horvath, M.P. / Goldenberg, D.P. | ||||||
![]() | ![]() Title: Structure of a serine protease poised to resynthesize a peptide bond. Authors: Zakharova, E. / Horvath, M.P. / Goldenberg, D.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.4 KB | Display | ![]() |
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PDB format | ![]() | 59.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.1 KB | Display | ![]() |
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Full document | ![]() | 465.9 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fp6C ![]() 3fp8C ![]() 3tgiS 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 on special symmetry positions |
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Details | AUTHORS STATE THAT THE QUATERNARY STRUCTURE IS A HETEROTRIMER. |
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Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 23798.838 Da / Num. of mol.: 1 / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Pancreatic trypsin ... , 2 types, 2 molecules IJ
#2: Protein/peptide | Mass: 1724.996 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: bovine pancreatic trypsin inhibitor was obtained in its hydrolyzed form by partial reduction at the cys14-cys38 disulfide, treatment with trypsin, purification by HPLC and re-oxidation of ...Details: bovine pancreatic trypsin inhibitor was obtained in its hydrolyzed form by partial reduction at the cys14-cys38 disulfide, treatment with trypsin, purification by HPLC and re-oxidation of the cys14-cys38 disulfide References: UniProt: P00974 |
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#3: Protein/peptide | Mass: 4820.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P00974 |
-Non-polymers , 5 types, 369 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-SO4 / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 295 K / pH: 8 Details: 0.2M lithium sulfate, 0.1M tris, 34% (w/v) PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Dec 3, 2007 / Details: OSMIC CONFOCAL MAX-FLUX (GREEN) |
Radiation | Monochromator: OSMIC CONFOCAL MAX-FLUX (GREEN) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→30 Å / Num. obs: 51853 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.9 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 6.7 / Rsym value: 0.205 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3TGI Resolution: 1.46→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: SIMULATED ANNEALING TORSION ANGLE REFINEMENT, POSITIONAL REFINEMENT, RESTRAINED ISOTROPIC INDIVIDUAL B-VALUE REFINEMENT, COUPLED WITH MODEL ADJUSTMENT ON THE BASIS OF SIGMA-A WEIGHTED AND ...Details: SIMULATED ANNEALING TORSION ANGLE REFINEMENT, POSITIONAL REFINEMENT, RESTRAINED ISOTROPIC INDIVIDUAL B-VALUE REFINEMENT, COUPLED WITH MODEL ADJUSTMENT ON THE BASIS OF SIGMA-A WEIGHTED AND COMPOSITE SIMULATED ANNEALING OMIT ELECTRON DENSITY MAPS
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Solvent computation | Solvent model: CNS SOLVE / Bsol: 33.26 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.46→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.55 Å / Total num. of bins used: 6
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Xplor file |
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