+Open data
-Basic information
Entry | Database: PDB / ID: 4kup | ||||||
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Title | Endothiapepsin in complex with 20mM acylhydrazone inhibitor | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Hydrolase / Aspartic protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.311 Å | ||||||
Authors | Radeva, N. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Structure-based design of inhibitors of the aspartic protease endothiapepsin by exploiting dynamic combinatorial chemistry. Authors: Mondal, M. / Radeva, N. / Koster, H. / Park, A. / Potamitis, C. / Zervou, M. / Klebe, G. / Hirsch, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kup.cif.gz | 142.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kup.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/4kup ftp://data.pdbj.org/pub/pdb/validation_reports/ku/4kup | HTTPS FTP |
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-Related structure data
Related structure data | 4lbtC 4lhhC 3pcwS 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: 33813.855 Da / Num. of mol.: 1 / Fragment: UNP residues 90-419 / Source method: isolated from a natural source Source: (natural) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, endothiapepsin |
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-Non-polymers , 5 types, 347 molecules
#2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.44 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2M ammonium acetate, 1M sodium acetate, 50% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2013 / Details: mirrors |
Radiation | Monochromator: Si-111 Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→30 Å / Num. all: 76831 / Num. obs: 76831 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.051 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.31→1.33 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 3792 / Rsym value: 0.401 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PCW Resolution: 1.311→26.78 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.03 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.311→26.78 Å
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Refine LS restraints |
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LS refinement shell |
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