+Open data
-Basic information
Entry | Database: PDB / ID: 3atl | ||||||
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Title | Crystal structure of trypsin complexed with benzamidine | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEASE / PROTEIN / INHIBITOR / BOVINE PANCREAS / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / digestion / serine protease inhibitor complex / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Yamane, J. / Yao, M. / Tanaka, I. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3atl.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3atl.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 3atl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/3atl ftp://data.pdbj.org/pub/pdb/validation_reports/at/3atl | HTTPS FTP |
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-Related structure data
Related structure data | 3atiC 3atkC 3atmC 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 (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) Bos taurus (cattle) / Tissue: pancreas / References: UniProt: P00760, trypsin | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | #4: Chemical | ChemComp-BEN / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.56 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
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: 1.74→50 Å / Num. all: 21074 / Num. obs: 21074 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.74→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2000 / Rsym value: 0.21 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A7T Resolution: 1.74→19.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.754 / SU ML: 0.058 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.105 / 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: 11.713 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Total num. of bins used: 20
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