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- PDB-2fi3: Crystal structure of a BPTI variant (Cys14->Ser, Cys38->Ser) in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fi3 | ||||||
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Title | Crystal structure of a BPTI variant (Cys14->Ser, Cys38->Ser) in complex with trypsin | ||||||
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![]() | hydrolase/hydrolase inhibitor / PROTEASE-INHIBITOR COMPLEX / hydrolase-hydrolase inhibitor COMPLEX | ||||||
Function / homology | ![]() trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zakharova, E. / Horvath, M.P. / Goldenberg, D.P. | ||||||
![]() | ![]() Title: Functional and structural roles of the Cys14-Cys38 disulfide of bovine pancreatic trypsin inhibitor. 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 | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 57.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fi4C ![]() 2fi5C ![]() 2ptcS 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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6 | ![]()
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7 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules EI
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 6495.438 Da / Num. of mol.: 1 / Mutation: C14S, C38S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid details: as described in Biochemistry 1988, 27, 2481-2489 Plasmid: pTI103 / Production host: ![]() ![]() |
-Non-polymers , 5 types, 266 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NA / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.34 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.75 M ammonium sulfate, 0.1 M HEPES, 0.02% sodium azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: NONIUS KAPPA CCD2000 / Detector: CCD / Date: Oct 23, 2004 / 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: 1.56→20 Å / Num. all: 54071 / Num. obs: 53322 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4633 / % possible all: 86.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PTC Resolution: 1.58→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber Details: Maximum-likelihood using measured intensities (mli) target implemented with CNS SOLVE 1.1
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Solvent computation | Bsol: 18.5858 Å2 / ksol: 0.360625 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.58→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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