+Open data
-Basic information
Entry | Database: PDB / ID: 2zq1 | ||||||
---|---|---|---|---|---|---|---|
Title | Exploring trypsin S3 pocket | ||||||
Components | Cationic trypsin | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Hydrolase inhibitors / Digestion / Hydrolase / Metal-binding / Protease / Secreted / Serine protease / Zymogen / Hydrolase-Hydrolase Inhibitor complex | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.68 Å | ||||||
Authors | Brandt, T. / Baum, B. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zq1.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zq1.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/2zq1 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/2zq1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2zdkSC 2zdlC 2zdmC 2zdnC 2zfsC 2zftC 2zhdC 2zq2C 3ljjC 3ljoC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) Bos taurus (cattle) / Tissue: Pancreas / References: UniProt: P00760, trypsin |
---|
-Non-polymers , 5 types, 173 molecules
#2: Chemical | ChemComp-CA / |
---|---|
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-11U / ( |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.033012 Å3/Da / Density % sol: 39.5 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Imidazole buffer, 0.1M ammonium sulfate, 30% PEG8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 103 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 30, 2008 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 21968 / % possible obs: 94.5 % / Redundancy: 1.8 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.052 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1481 / Rsym value: 0.359 / % possible all: 71.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2ZDK Resolution: 1.68→10 Å / Num. parameters: 7358 / Num. restraintsaints: 6903 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 1571 / Occupancy sum non hydrogen: 1823 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|