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- PDB-8q10: Endothiapepsin in complex with ligand (3R,5R)-3-(2-(hydroxymethyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q10 | ||||||
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Title | Endothiapepsin in complex with ligand (3R,5R)-3-(2-(hydroxymethyl)thiazol-4-yl)-5-(3-(4-(trifluoromethyl)phenyl)-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol (CBWS-SE-125) | ||||||
![]() | Endothiapepsin | ||||||
![]() | HYDROLASE / Endothiapepsin / ligand complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mueller, J.M. / Eckelt, S. / Klebe, G. / Glinca, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structures of Endothiapepsin with ligands derived from merged fragment hits Authors: Mueller, J.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 | ![]() | 174.1 KB | Display | ![]() |
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PDB format | ![]() | 112.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 749.6 KB | Display | ![]() |
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Full document | ![]() | 749.6 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pxiC ![]() 8q0vC ![]() 8q0wC ![]() 8q0xC ![]() 8q0yC ![]() 8q0zC ![]() 8q11C ![]() 8q12C ![]() 8q13C ![]() 8q14C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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 , 7 types, 227 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-IJY / ( Mass: 412.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15F3N4O3S / Feature type: SUBJECT OF INVESTIGATION | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-MPD / ( | #7: Chemical | ChemComp-PGE / | #8: 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: 2.38 Å3/Da / Density % sol: 48.33 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Protein at 5 mg/mL in 100 mM ammoniumacetate pH 4.6, reservoir: 100 mM ammoniumacetate, 100 mM sodium acetate pH 4.6, 24 % PEG4000, 292 K, 2+2 yL drops over 1 mL reservoir, streak seeding |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→50 Å / Num. obs: 83117 / % possible obs: 99.3 % / Redundancy: 3.77 % / Biso Wilson estimate: 14.43 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.79 |
Reflection shell | Resolution: 1.27→1.35 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 13272 / CC1/2: 0.813 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.27→27.97 Å
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Refine LS restraints |
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LS refinement shell |
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