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- PDB-9g35: The HIV protease inhibitor lopinavir binding to the active site o... -

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Basic information

Entry
Database: PDB / ID: 9g35
TitleThe HIV protease inhibitor lopinavir 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


endothiapepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-AB1 / TRIETHYLENE GLYCOL / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 lopinavir binding to the active site of Cryphonectria parasitica endothiapepsin
Authors: Falke, S. / Senst, J.M. / Guenther, S. / Meents, A.
History
DepositionJul 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1057
Polymers33,8141
Non-polymers1,2926
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint17 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.539, 73.519, 53.410
Angle α, β, γ (deg.)90.000, 110.139, 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 natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin

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Non-polymers , 5 types, 393 molecules

#2: Chemical ChemComp-AB1 / N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE / ABT-378 / LOPINAVIR


Mass: 628.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N4O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiretroviral, protease inhibitor*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.45 %
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: 1.03319 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.5→42.75 Å / Num. obs: 101583 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 11.07 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.047 / Net I/σ(I): 20.77
Reflection shellResolution: 1.5→1.54 Å / Num. unique obs: 7716 / CC1/2: 0.987 / Rrim(I) all: 0.113

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.18_3861phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→42.75 Å / SU ML: 0.1167 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 14.5396
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1588 1999 1.97 %
Rwork0.1497 99580 -
obs0.1499 101579 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.49 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 90 387 2866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542586
X-RAY DIFFRACTIONf_angle_d0.82163532
X-RAY DIFFRACTIONf_chiral_restr0.0572411
X-RAY DIFFRACTIONf_plane_restr0.0057454
X-RAY DIFFRACTIONf_dihedral_angle_d8.2261428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.16971640.14937091X-RAY DIFFRACTION97.8
1.54-1.580.17671430.14336987X-RAY DIFFRACTION95.63
1.58-1.630.1931520.14767250X-RAY DIFFRACTION98.83
1.63-1.680.18951270.14287180X-RAY DIFFRACTION98.86
1.68-1.740.16581470.15037168X-RAY DIFFRACTION98.56
1.74-1.810.16651470.15027161X-RAY DIFFRACTION98.19
1.81-1.890.18511410.15937151X-RAY DIFFRACTION97.72
1.89-1.990.16041260.14897098X-RAY DIFFRACTION97.16
1.99-2.110.15991340.15176898X-RAY DIFFRACTION94.35
2.11-2.280.15521470.14537106X-RAY DIFFRACTION97.34
2.28-2.510.16011400.167195X-RAY DIFFRACTION98.81
2.51-2.870.18321390.16177175X-RAY DIFFRACTION98.47
2.87-3.610.15991410.15697046X-RAY DIFFRACTION96.69
3.62-42.750.12061510.13297074X-RAY DIFFRACTION96.91

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