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- PDB-8q0x: Endothiapepsin in complex with ligand (3R,5R)-3-(2-((methyl(propy... -

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Basic information

Entry
Database: PDB / ID: 8q0x
TitleEndothiapepsin in complex with ligand (3R,5R)-3-(2-((methyl(propyl)amino)methyl)thiazol-4-yl)-5-(3-(4-(trifluoromethyl)phenyl)-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol (CBWS-SE-087)
ComponentsEndothiapepsin
KeywordsHYDROLASE / Endothiapepsin / ligand complex
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
ACETATE ION / : / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsMueller, J.M. / Eckelt, S. / Klebe, G. / Glinca, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structures of Endothiapepsin with ligands derived from merged fragment hits
Authors: Mueller, J.M.
History
DepositionJul 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7128
Polymers33,8141
Non-polymers8987
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint6 kcal/mol
Surface area12760 Å2
Unit cell
Length a, b, c (Å)44.923, 72.561, 52.503
Angle α, β, γ (deg.)90.000, 109.190, 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

#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
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-IL4 / (3~{R},5~{R})-3-[2-[[methyl(propyl)amino]methyl]-1,3-thiazol-4-yl]-5-[3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]pyrrolidin-3-ol


Mass: 467.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24F3N5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein at 5 mg/mL in 100 mM ammoniumacetate pH 4.6, reservoir: 100 mM ammoniumacetate, 100 mM sodium acetate pH 4.6, 24 % PEG4000, 292 K, 2+2 yL drops over 1 mL reservoir, streak seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99187 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 82604 / % possible obs: 99.1 % / Redundancy: 3.74 % / Biso Wilson estimate: 14.56 Å2 / CC1/2: 0.994 / Net I/σ(I): 8.97
Reflection shellResolution: 1.275→1.35 Å / Redundancy: 3.69 % / Mean I/σ(I) obs: 2 / Num. unique obs: 12980 / CC1/2: 0.807 / % possible all: 96.8

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→34.51 Å / SU ML: 0.1409 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 15.518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1656 4131 5 %
Rwork0.1428 78466 -
obs0.144 82597 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.17 Å2
Refinement stepCycle: LAST / Resolution: 1.27→34.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 56 252 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182562
X-RAY DIFFRACTIONf_angle_d1.19343531
X-RAY DIFFRACTIONf_chiral_restr0.1019413
X-RAY DIFFRACTIONf_plane_restr0.0091455
X-RAY DIFFRACTIONf_dihedral_angle_d12.3831824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.290.28431180.23462232X-RAY DIFFRACTION85.05
1.29-1.30.23751360.21422585X-RAY DIFFRACTION99.89
1.3-1.320.23371410.19922670X-RAY DIFFRACTION99.79
1.32-1.330.29591370.20442609X-RAY DIFFRACTION99.82
1.33-1.350.22451370.21962607X-RAY DIFFRACTION99.71
1.35-1.370.23641380.20222618X-RAY DIFFRACTION99.71
1.37-1.390.21281390.17582638X-RAY DIFFRACTION99.82
1.39-1.410.2071370.15932605X-RAY DIFFRACTION99.89
1.41-1.430.19951380.14562629X-RAY DIFFRACTION99.86
1.43-1.460.17681390.13862641X-RAY DIFFRACTION99.89
1.46-1.480.19451370.13352590X-RAY DIFFRACTION99.67
1.48-1.510.17311380.12792632X-RAY DIFFRACTION99.75
1.51-1.540.16361380.11792624X-RAY DIFFRACTION99.6
1.54-1.570.14721380.11882611X-RAY DIFFRACTION99.78
1.57-1.60.14171390.11982643X-RAY DIFFRACTION99.82
1.6-1.640.14951380.12262616X-RAY DIFFRACTION99.85
1.64-1.680.15221380.11842632X-RAY DIFFRACTION99.96
1.68-1.730.14771400.1192667X-RAY DIFFRACTION99.79
1.73-1.780.13821370.11242598X-RAY DIFFRACTION99.78
1.78-1.840.1411380.11432619X-RAY DIFFRACTION99.67
1.84-1.90.1631390.11732641X-RAY DIFFRACTION99.64
1.9-1.980.12551370.1172598X-RAY DIFFRACTION99.64
1.98-2.070.13481380.11712635X-RAY DIFFRACTION99.32
2.07-2.180.15751390.1182631X-RAY DIFFRACTION99.68
2.18-2.310.14551380.12792629X-RAY DIFFRACTION99.86
2.31-2.490.16481400.14332665X-RAY DIFFRACTION99.72
2.49-2.740.18051380.15022611X-RAY DIFFRACTION99.67
2.74-3.140.19481390.15832652X-RAY DIFFRACTION99.68
3.14-3.950.15371400.15492645X-RAY DIFFRACTION99.39
3.95-34.510.16521420.16562693X-RAY DIFFRACTION99.3

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