[English] 日本語
Yorodumi- PDB-3aav: Bovine beta-trypsin bound to meta-diamidino schiff base copper (I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aav | ||||||
---|---|---|---|---|---|---|---|
Title | Bovine beta-trypsin bound to meta-diamidino schiff base copper (II) chelate | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / enzyme-inhibitor complex / coordination metal based inhibitor / Calcium / Digestion / Metal-binding / Protease / Secreted / Serine protease / Zymogen | ||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Iyaguchi, D. / Kawano, S. / Toyota, E. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: Structural basis for the design of novel Schiff base metal chelate inhibitors of trypsin Authors: Iyaguchi, D. / Kawano, S. / Takada, K. / Toyota, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3aav.cif.gz | 105 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3aav.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 3aav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/3aav ftp://data.pdbj.org/pub/pdb/validation_reports/aa/3aav | HTTPS FTP |
---|
-Related structure data
Related structure data | 3aasC 3aauC 1g3dS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.75 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 39258 / % possible obs: 99.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.213 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G3D Resolution: 1.7→20 Å
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
|