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- PDB-3atm: Crystal structure of trypsin complexed with 2-(1H-indol-3-yl)etha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3atm | ||||||
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Title | Crystal structure of trypsin complexed with 2-(1H-indol-3-yl)ethanamine | ||||||
![]() | Cationic trypsin | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEASE / PROTEIN / INHIBITOR / BOVINE PANCREAS / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities Authors: Yamane, J. / Yao, M. / Zhou, Y. / Hiramatsu, Y. / Fujiwara, K. / Yamaguchi, T. / Yamaguchi, H. / Togame, H. / Tsujishita, H. / 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 | ![]() | 64.3 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.8 KB | Display | ![]() |
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Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3atiC ![]() 3atkC ![]() 3atlC ![]() 3rxaC ![]() 3rxbC ![]() 3rxcC ![]() 3rxdC ![]() 3rxeC ![]() 3rxfC ![]() 3rxgC ![]() 3rxhC ![]() 3rxiC ![]() 3rxjC ![]() 3rxkC ![]() 3rxlC ![]() 3rxmC ![]() 3rxoC ![]() 3rxpC ![]() 3rxqC ![]() 3rxrC ![]() 3rxsC ![]() 3rxtC ![]() 3rxuC ![]() 3rxvC ![]() 3a7tS 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
#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 | #4: Chemical | ChemComp-TSS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.55 % |
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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 IV / 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: 1.72→50 Å / Num. all: 22247 / Num. obs: 22247 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 40.6 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 6 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 18.5 / Num. unique all: 2056 / Rsym value: 0.077 / % possible all: 90.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A7T Resolution: 1.72→19.85 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.557 / SU ML: 0.052 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.093 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.571 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.764 Å / Total num. of bins used: 20
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