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Open data
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Basic information
Entry | Database: PDB / ID: 2zdk | ||||||
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Title | Exploring Trypsin S3 Pocket | ||||||
![]() | Cationic trypsin | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / Hydrolase Inhibitors / Digestion / Metal-binding / Protease / Secreted / Serine protease / Zymogen / 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 | ![]() ![]() | ||||||
![]() | Baum, B. / Brandt, T. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties Authors: Brandt, T. / Holzmann, N. / Muley, L. / Khayat, M. / Wegscheid-Gerlach, C. / Baum, B. / Heine, A. / Hangauer, D. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.2 KB | Display | ![]() |
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PDB format | ![]() | 44.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 781.3 KB | Display | ![]() |
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Full document | ![]() | 783.4 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zdlC ![]() 2zdmC ![]() 2zdnC ![]() 2zfsC ![]() 2zftC ![]() 2zhdC ![]() 2zq1C ![]() 2zq2C ![]() 3ljjC ![]() 3ljoC ![]() 1gi1S 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 240 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/50U.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/50U.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||
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#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | ChemComp-50U / ( | ||
#5: Chemical | ChemComp-DMS / | ||
#6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Imidazole buffer, 0.1M ammonium sulfate, 25% PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→30 Å / Num. all: 22193 / Num. obs: 22193 / % possible obs: 98.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 15.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 944 / Rsym value: 0.356 / % possible all: 83.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1GI1 Resolution: 1.67→10 Å / Num. parameters: 7832 / Num. restraintsaints: 7161 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 1566 / Occupancy sum non hydrogen: 1921.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→10 Å
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Refine LS restraints |
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