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- PDB-3a80: Crystal Structure of Trypsin complexed with (E)-2-(4-carbamimidoy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a80 | ||||||
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Title | Crystal Structure of Trypsin complexed with (E)-2-(4-carbamimidoylbenzylideneaminooxy)-2-methylpropanoic acid (soaking 40seconds) | ||||||
![]() | Cationic trypsin | ||||||
![]() | HYDROLASE / In-Crystal Chemical Ligation / Digestion / Disulfide bond / Metal-binding / Protease / Secreted / Serine protease / Zymogen | ||||||
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 | ![]() ![]() | ||||||
![]() | Yamane, J. / Yao, M. / Tanaka, I. | ||||||
![]() | ![]() Title: In-Crystal Chemical Ligation for Drug Discovery Authors: Yamane, J. / Ooyabu, N. / Yao, M. / Takemoto, H. / Tanaka, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.2 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.6 KB | Display | ![]() |
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Full document | ![]() | 434.2 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a7tSC ![]() 3a7vC ![]() 3a7wC ![]() 3a7xC ![]() 3a7yC ![]() 3a7zC ![]() 3a81C ![]() 3a82C ![]() 3a83C ![]() 3a84C ![]() 3a85C ![]() 3a86C ![]() 3a87C ![]() 3a88C ![]() 3a89C ![]() 3a8aC ![]() 3a8bC ![]() 3a8cC ![]() 3a8dC 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
#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-O15 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl, 30% PEG 3350, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.289 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A7T Resolution: 1.75→19.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.939 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.297 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.748→1.793 Å / Total num. of bins used: 20
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