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- PDB-7bkv: Endothiapepsin structure obtained at 100K with fragment AC39729 bound -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bkv | ||||||
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Title | Endothiapepsin structure obtained at 100K with fragment AC39729 bound | ||||||
![]() | Endothiapepsin | ||||||
![]() | HYDROLASE / FBDD / inhibitor | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Engilberge, S. / Huang, C.-Y. / Smith, K.M.L. / Eris, D. / Marsh, M. / Wang, M. / Wojdyla, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Endothiapepsin structure obtained at 100K with fragment AC39729 bound Authors: Engilberge, S. / Huang, C.-Y. / Smith, K.M.L. / Eris, D. / Wojdyla, J.A. / Olieric, V. / Leonarski, F. / Sharpe, M. / Wang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93 KB | Display | ![]() |
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PDB format | ![]() | 67.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 740.3 KB | Display | ![]() |
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Full document | ![]() | 740.7 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rsvS 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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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 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P11838, endothiapepsin |
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-Non-polymers , 5 types, 577 molecules ![](data/chem/img/U1Q.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-U1Q / | ||||||
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#3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 100 mM ammonium acetate, 100 mM sodium acetate pH 4.6 and 26 to 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→42.58 Å / Num. obs: 70862 / % possible obs: 77.09 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rpim(I) all: 0.0209 / Net I/σ(I): 19.22 |
Reflection shell | Resolution: 1.24→1.28 Å / Mean I/σ(I) obs: 1.51 / Num. unique obs: 4490 / CC1/2: 0.72 / Rpim(I) all: 0.4482 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6RSV Resolution: 1.24→42.58 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.76 / 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: 70.95 Å2 / Biso mean: 17.9482 Å2 / Biso min: 1.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.24→42.58 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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