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Yorodumi- PDB-8q4b: Endothiapepsin in complex with ligand (3R,5R)-3-(2-((methyl(prop-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q4b | ||||||
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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-(2-nitrophenyl)-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol (CBWS-SE-163.1) | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / Endothiapepsin / ligand complex | ||||||
Function / homology | Function and homology information 4-hydroxy-3-polyprenylbenzoate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Mueller, J.M. / Eckelt, S. / Klebe, G. / Glinca, S. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q4b.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q4b.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 8q4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q4b_validation.pdf.gz | 728.5 KB | Display | wwPDB validaton report |
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Full document | 8q4b_full_validation.pdf.gz | 729.9 KB | Display | |
Data in XML | 8q4b_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 8q4b_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/8q4b ftp://data.pdbj.org/pub/pdb/validation_reports/q4/8q4b | HTTPS FTP |
-Related structure data
Related structure data | 8pxiC 8q0vC 8q0wC 8q0xC 8q0yC 8q0zC 8q10C 8q11C 8q12C 8q13C 8q14C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, EC: 3.4.23.22 |
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-Non-polymers , 6 types, 257 molecules
#2: Chemical | ChemComp-JCI / ( Mass: 426.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N6O4S / Feature type: SUBJECT OF INVESTIGATION | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % |
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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: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.688813 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.688813 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→50 Å / Num. obs: 75363 / % possible obs: 93.4 % / Redundancy: 3.73 % / Biso Wilson estimate: 15.73 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.04 |
Reflection shell | Resolution: 1.28→1.36 Å / Redundancy: 3.68 % / Mean I/σ(I) obs: 1.09 / Num. unique obs: 11963 / CC1/2: 0.615 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→36.68 Å / SU ML: 0.1651 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0949 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: 22.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→36.68 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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