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- PDB-8q0z: Endothiapepsin in complex with ligand (3R,5R)-3-(2-((methyl(prop-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q0z | ||||||
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Title | Endothiapepsin in complex with ligand (3R,5R)-3-(2-((methyl(prop-2-yn-1-yl)amino)methyl)thiazol-4-yl)-5-(3-phenyl-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol (CBWS-SE-089) | ||||||
![]() | 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 | ![]() | 175.2 KB | Display | ![]() |
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PDB format | ![]() | 113.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 923.3 KB | Display | ![]() |
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Full document | ![]() | 925 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pxiC ![]() 8q0vC ![]() 8q0wC ![]() 8q0xC ![]() 8q0yC ![]() 8q10C ![]() 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 , 5 types, 270 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | Mass: 395.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N5O2S / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.47 % |
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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: 1.21→50 Å / Num. obs: 94958 / % possible obs: 98.1 % / Redundancy: 3.67 % / Biso Wilson estimate: 11.51 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.86 |
Reflection shell | Resolution: 1.21→1.28 Å / Redundancy: 3.13 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 14055 / CC1/2: 0.955 / % possible all: 90.1 |
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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: 14.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.21→29.28 Å
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Refine LS restraints |
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LS refinement shell |
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