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Yorodumi- PDB-9g34: The HIV protease inhibitor darunavir binding to the active site o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9g34 | |||||||||
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Title | The HIV protease inhibitor darunavir binding to the active site of Cryphonectria parasitica endothiapepsin | |||||||||
Components | Endothiapepsin | |||||||||
Keywords | HYDROLASE / aspartic protease / drug development / inhibitor / X-ray crystallographic screening / chestnut blight fungus / distinct unit cell | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Falke, S. / Senst, J.M. / Guenther, S. / Meents, A. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: To Be Published Title: The HIV protease inhibitor darunavir binding to the active site of Cryphonectria parasitica endothiapepsin Authors: Falke, S. / Senst, J.M. / Guenther, S. / Meents, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9g34.cif.gz | 194.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9g34.ent.gz | 123.1 KB | Display | PDB format |
PDBx/mmJSON format | 9g34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9g34_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9g34_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 9g34_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 9g34_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/9g34 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/9g34 | HTTPS FTP |
-Related structure data
Related structure data | |
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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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33813.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, endothiapepsin |
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-Non-polymers , 5 types, 913 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-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: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow | Temperature: 291 K / Method: batch mode Details: 30 mg/ml endothiapepsin in 0.1 M sodium acetate at pH 4.6 was mixed with an equal volume of crystallisation solution, i.e. 0.1 M Tris-HCl pH 7.0, 0.15 M MgCl2, 30% PEG 6000. Microseeding was ...Details: 30 mg/ml endothiapepsin in 0.1 M sodium acetate at pH 4.6 was mixed with an equal volume of crystallisation solution, i.e. 0.1 M Tris-HCl pH 7.0, 0.15 M MgCl2, 30% PEG 6000. Microseeding was applied. Crystals were soaked with the ligand in the presence of 5% (v/v) DMSO. |
-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: 1.03319 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 3, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→45.41 Å / Num. obs: 159326 / % possible obs: 98.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.42 Å2 / CC1/2: 1 / Rrim(I) all: 0.032 / Net I/σ(I): 30.03 |
Reflection shell | Resolution: 1.3→1.32 Å / Num. unique obs: 6492 / CC1/2: 0.982 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.41 Å / SU ML: 0.0947 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.7637 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 13.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→45.41 Å
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Refine LS restraints |
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LS refinement shell |
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