+Open data
-Basic information
Entry | Database: PDB / ID: 2zdl | ||||||
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Title | Exploring trypsin S3 pocket | ||||||
Components | Cationic trypsin | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Hydrolase Inhibitors / Digestion / 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: 1.8 Å | ||||||
Authors | Baum, B. / Brandt, T. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zdl.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zdl.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zdl_validation.pdf.gz | 742.4 KB | Display | wwPDB validaton report |
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Full document | 2zdl_full_validation.pdf.gz | 744.6 KB | Display | |
Data in XML | 2zdl_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 2zdl_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/2zdl ftp://data.pdbj.org/pub/pdb/validation_reports/zd/2zdl | HTTPS FTP |
-Related structure data
Related structure data | 2zdkC 2zdmC 2zdnC 2zfsC 2zftC 2zhdC 2zq1C 2zq2C 3ljjC 3ljoC 1gi1S 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
-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 |
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-Non-polymers , 5 types, 170 molecules
#2: Chemical | ChemComp-CA / | ||
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#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | ChemComp-45U / ( | ||
#5: Chemical | #6: 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 Å3/Da / Density % sol: 38.38 % |
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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: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.00001 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2007 |
Radiation | Monochromator: Double crystal Si[111], horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 16745 / Num. obs: 16745 / % possible obs: 93.1 % / Redundancy: 4 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.085 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 813 / Rsym value: 0.383 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 1GI1 Resolution: 1.8→10 Å / Num. parameters: 7492 / Num. restraintsaints: 7141 / 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: 7 / Occupancy sum hydrogen: 1582 / Occupancy sum non hydrogen: 1835.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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