+Open data
-Basic information
Entry | Database: PDB / ID: 5hct | ||||||
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Title | Endothiapepsin in complex with biacylhydrazone | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / inhibition | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.36 Å | ||||||
Authors | Radeva, N. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 Title: Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment-Based Drug Design Facilitated by Dynamic Combinatorial Chemistry. Authors: Mondal, M. / Radeva, N. / Fanlo-Virgos, H. / Otto, S. / Klebe, G. / Hirsch, A.K. #1: 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. / Koester, 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 | 5hct.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hct.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 5hct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/5hct ftp://data.pdbj.org/pub/pdb/validation_reports/hc/5hct | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 43278.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, endothiapepsin |
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-Non-polymers , 7 types, 242 molecules
#2: Chemical | ChemComp-DMS / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-61P / | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.18 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystals obtained by streak-seeding |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→42.79 Å / Num. obs: 69237 / % possible obs: 99.6 % / Redundancy: 3.77 % / Rsym value: 0.066 / Net I/σ(I): 11.27 |
Reflection shell | Resolution: 1.36→1.44 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.41 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Resolution: 1.36→42.79 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.73 / Stereochemistry target values: ML
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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: 1.36→42.79 Å
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Refine LS restraints |
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LS refinement shell |
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