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- PDB-1y1k: Crystal structure of the complex of subtilisin BPN' with chymotry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y1k | ||||||
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Title | Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 T58A mutant | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / serine protease / inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Radisky, E.S. / Lu, C.J. / Kwan, G. / Koshland Jr., D.E. | ||||||
![]() | ![]() Title: Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2 Authors: Radisky, E.S. / Lu, C.J. / Kwan, G. / Koshland Jr., D.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.4 KB | Display | ![]() |
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PDB format | ![]() | 70 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y33C ![]() 1y34C ![]() 1y3bC ![]() 1y3cC ![]() 1y3dC ![]() 1y3fC ![]() 1y48C ![]() 1y4aC ![]() 1y4dC ![]() 1tm3S C: citing same article ( S: Starting model for refinement |
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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 , 2 types, 2 molecules EI
#1: Protein | Mass: 28381.396 Da / Num. of mol.: 1 / Mutation: C-terminal 6-His tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 7253.575 Da / Num. of mol.: 1 / Mutation: initiating Met, T58A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 507 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/15P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/15P.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | ChemComp-NA / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium citrate, isopropanol, PEG 2000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→81.65 Å / Num. all: 69911 / Num. obs: 69911 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.07 / Net I/σ(I): 13.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TM3 Resolution: 1.56→81.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.157 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.283 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→81.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.601 Å / Total num. of bins used: 20 /
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