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- PDB-9fvo: The HIV protease inhibitor amprenavir binding to the active site ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9fvo | |||||||||
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Title | The HIV protease inhibitor amprenavir binding to the active site of Cryphonectria parasitica endothiapepsin | |||||||||
![]() | Endothiapepsin | |||||||||
![]() | HYDROLASE / aspartic protease / drug development / inhibitor / X-ray crystallographic screening / chestnut blight fungus / protease model. | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Falke, S. / Senst, J.M. / Guenther, S. / Meents, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The HIV protease inhibitor amprenavir 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.5 KB | Display | ![]() |
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PDB format | ![]() | 105.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 782.8 KB | Display | ![]() |
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Full document | ![]() | 785.1 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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 genetically manipulated source Source: (gene. exp.) ![]() Gene: EAPA, EPN-1 Production host: ![]() References: UniProt: P11838, EC: 3.4.23.22 |
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-Non-polymers , 6 types, 306 molecules ![](data/chem/img/478.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-478 / { | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.47 Å3/Da / Density % sol: 50.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 24% (w/v) PEG 4000, 0.1 M ammonium acetate and 0.1 M sodium acetate pH 4.6 were mixed with an equal volume of 6 mg/ml endothiapepsin solution. Microseeding was applied. After 2 days crystals ...Details: 24% (w/v) PEG 4000, 0.1 M ammonium acetate and 0.1 M sodium acetate pH 4.6 were mixed with an equal volume of 6 mg/ml endothiapepsin solution. Microseeding was applied. After 2 days crystals were soaked with the ligand in reservoir solution 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 16, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.826501 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.03 Å / Num. obs: 30224 / % possible obs: 98.9 % / Redundancy: 13.69 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.087 / Net I/σ(I): 23.75 |
Reflection shell | Resolution: 1.8→1.84 Å / Num. unique obs: 1928 / CC1/2: 0.99 / Rrim(I) all: 0.225 |
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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: 16.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→43.03 Å
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Refine LS restraints |
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LS refinement shell |
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