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- PDB-3wz8: Endothiapepsin in complex with Gewald reaction-derived inhibitor (8) -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wz8 | ||||||
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Title | Endothiapepsin in complex with Gewald reaction-derived inhibitor (8) | ||||||
![]() | Endothiapepsin | ||||||
![]() | Hydrolase/Hydrolase inhibitor / aspartic protease / Hydrolase-Hydrolase inhibitor complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuhnert, M. / Steuber, H. / Diederich, W.E. | ||||||
![]() | ![]() Title: Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors Authors: Kuhnert, M. / Koster, H. / Bartholomaus, R. / Park, A.Y. / Shahim, A. / Heine, A. / Steuber, H. / Klebe, G. / Diederich, W.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.7 KB | Display | ![]() |
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PDB format | ![]() | 65.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726.2 KB | Display | ![]() |
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Full document | ![]() | 726.5 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3psyC ![]() 3wz6C ![]() 3wz7C ![]() 1oewS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P11838, endothiapepsin |
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#2: Chemical | ChemComp-IXV / |
#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-DMS / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: ammonium acetate, PEG4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2013 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 59674 / Num. obs: 59674 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.65 Å2 |
Reflection shell | Resolution: 1.45→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.6 / Num. unique all: 15187 / Rsym value: 0.567 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OEW Resolution: 1.45→40.442 Å / FOM work R set: 0.829 / SU ML: 0.18 / σ(F): 0 / Phase error: 24.5 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.74 Å2 / Biso mean: 10.69 Å2 / Biso min: 1.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→40.442 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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