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- PDB-9fvo: The HIV protease inhibitor amprenavir binding to the active site ... -

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Basic information

Entry
Database: PDB / ID: 9fvo
TitleThe HIV protease inhibitor amprenavir binding to the active site of Cryphonectria parasitica endothiapepsin
ComponentsEndothiapepsin
KeywordsHYDROLASE / aspartic protease / drug development / inhibitor / X-ray crystallographic screening / chestnut blight fungus / protease model.
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
UbiD decarboxylyase, bacteria / : / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain
Similarity search - Domain/homology
Chem-478 / ACETIC ACID / TRIETHYLENE GLYCOL / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFalke, S. / Senst, J.M. / Guenther, S. / Meents, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
Helmholtz Association Germany
German Federal Ministry for Education and Research Germany
CitationJournal: To Be Published
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
DepositionJun 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,50912
Polymers33,8141
Non-polymers1,69511
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint28 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.638, 72.832, 53.230
Angle α, β, γ (deg.)90.000, 109.460, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endothiapepsin / Aspartate protease


Mass: 33813.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryphonectria parasitica (chestnut blight fungus)
Gene: EAPA, EPN-1
Production host: Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, EC: 3.4.23.22

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Non-polymers , 6 types, 306 molecules

#2: Chemical ChemComp-478 / {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER / Amprenavir


Mass: 505.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: protease inhibitor, medication*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.826501 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826501 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.8→1.84 Å / Num. unique obs: 1928 / CC1/2: 0.99 / Rrim(I) all: 0.225

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Processing

Software
NameVersionClassification
PHENIX1.20-4459-9999refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.20-4459-9999phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.03 Å / SU ML: 0.1518 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1715 2000 6.65 %
Rwork0.1408 28097 -
obs0.1428 30097 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 114 295 2798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242604
X-RAY DIFFRACTIONf_angle_d1.00573545
X-RAY DIFFRACTIONf_chiral_restr0.0696411
X-RAY DIFFRACTIONf_plane_restr0.0072449
X-RAY DIFFRACTIONf_dihedral_angle_d9.8178436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.21861440.15892015X-RAY DIFFRACTION99.58
1.85-1.890.17661420.15152006X-RAY DIFFRACTION99.58
1.89-1.950.17021420.13961999X-RAY DIFFRACTION99.07
1.95-2.010.20351450.13252019X-RAY DIFFRACTION99.18
2.01-2.090.18041390.13281964X-RAY DIFFRACTION96.82
2.09-2.170.17711360.13221907X-RAY DIFFRACTION94.8
2.17-2.270.171440.13812026X-RAY DIFFRACTION99.68
2.27-2.390.15931450.13322034X-RAY DIFFRACTION99.41
2.39-2.540.15591430.13742019X-RAY DIFFRACTION99.4
2.54-2.730.18561440.14432011X-RAY DIFFRACTION99.68
2.73-3.010.17441450.15382033X-RAY DIFFRACTION99.45
3.01-3.440.17161430.15712026X-RAY DIFFRACTION99.68
3.44-4.340.16751390.13191947X-RAY DIFFRACTION95.25
4.34-43.030.15471490.13532091X-RAY DIFFRACTION99.82

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