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- PDB-9g34: The HIV protease inhibitor darunavir binding to the active site o... -

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Basic information

Entry
Database: PDB / ID: 9g34
TitleThe HIV protease inhibitor darunavir binding to the active site of Cryphonectria parasitica endothiapepsin
ComponentsEndothiapepsin
KeywordsHYDROLASE / aspartic protease / drug development / inhibitor / X-ray crystallographic screening / chestnut blight fungus / distinct unit cell
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-017 / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 darunavir 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

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
B: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9879
Polymers67,6282
Non-polymers1,3607
Water16,322906
1
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4634
Polymers33,8141
Non-polymers6493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5255
Polymers33,8141
Non-polymers7114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.654, 72.336, 101.942
Angle α, β, γ (deg.)90.000, 95.873, 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, 2 molecules AB

#1: Protein Endothiapepsin / Aspartate protease


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 ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37N3O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 906 / 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: 50.32 %
Crystal growTemperature: 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.

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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: 1.3→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 shellResolution: 1.3→1.32 Å / Num. unique obs: 6492 / CC1/2: 0.982

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1-4487phasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1715 3181 1.02 %
Rwork0.1579 309473 -
obs0.1581 159242 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.91 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 90 906 5774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00445206
X-RAY DIFFRACTIONf_angle_d0.77557176
X-RAY DIFFRACTIONf_chiral_restr0.077847
X-RAY DIFFRACTIONf_plane_restr0.0051923
X-RAY DIFFRACTIONf_dihedral_angle_d6.5746852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.22291230.19111798X-RAY DIFFRACTION86.26
1.32-1.340.19431400.181213316X-RAY DIFFRACTION96.09
1.34-1.360.21341380.176913555X-RAY DIFFRACTION98.87
1.36-1.390.18021420.170513615X-RAY DIFFRACTION98.96
1.39-1.410.18451360.163413439X-RAY DIFFRACTION98.67
1.41-1.440.16511410.159413609X-RAY DIFFRACTION98.62
1.44-1.470.14921390.155813535X-RAY DIFFRACTION98.5
1.47-1.50.17591400.152813500X-RAY DIFFRACTION98.41
1.5-1.530.16461400.153213466X-RAY DIFFRACTION97.81
1.53-1.570.1611370.152413382X-RAY DIFFRACTION97.26
1.57-1.610.15871360.153613284X-RAY DIFFRACTION96.87
1.61-1.660.18021380.150613604X-RAY DIFFRACTION99.47
1.66-1.720.16991400.159613687X-RAY DIFFRACTION99.46
1.72-1.780.1991420.166413617X-RAY DIFFRACTION99.21
1.78-1.850.23871410.16413719X-RAY DIFFRACTION99.13
1.85-1.930.18981340.160813493X-RAY DIFFRACTION98.65
1.93-2.030.18431410.154613542X-RAY DIFFRACTION98.18
2.03-2.160.14411400.155813290X-RAY DIFFRACTION96.81
2.16-2.330.16821380.15513516X-RAY DIFFRACTION98.58
2.33-2.560.17351390.169613695X-RAY DIFFRACTION99.81
2.56-2.930.1851410.169313708X-RAY DIFFRACTION99.83
2.93-3.70.17821350.157213653X-RAY DIFFRACTION99.04
3.7-45.410.13281400.138913450X-RAY DIFFRACTION97.97

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