+Open data
-Basic information
Entry | Database: PDB / ID: 2zhd | ||||||
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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 / FOURIER SYNTHESIS / Resolution: 1.94 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zhd.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zhd.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/2zhd ftp://data.pdbj.org/pub/pdb/validation_reports/zh/2zhd | HTTPS FTP |
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-Related structure data
Related structure data | 2zdkC 2zdlC 2zdmC 2zdnC 2zfsC 2zftC 2zq1C 2zq2C 3ljjC 3ljoC 1k1pS 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, 155 molecules
#2: Chemical | ChemComp-CA / | ||
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#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | ChemComp-12U / | ||
#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: 2.89 Å3/Da / Density % sol: 57.44 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.9M Ammonium sulfate, 50mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. all: 18886 / Num. obs: 18886 / % possible obs: 91.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.097 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 716 / Rsym value: 0.363 / % possible all: 70.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1K1P Resolution: 1.94→10 Å / Num. parameters: 7551 / Num. restraintsaints: 7230 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 1591 / Occupancy sum non hydrogen: 1833 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→10 Å
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Refine LS restraints |
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