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- PDB-7if4: Crystal structure of Endothiapepsin in complex with fragment EOS1... -

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Basic information

Entry
Database: PDB / ID: 7if4
TitleCrystal structure of Endothiapepsin in complex with fragment EOS103110 from ECBL-96
ComponentsEndothiapepsin
KeywordsHYDROLASE / crystallographic fragment screening / Endothiapepsin / ECBL-96 fragment library
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 / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsWollenhaupt, J. / Benz, L.S. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission871037European Union
CitationJournal: Rsc Med Chem / Year: 2025
Title: From fragments to follow-ups: rapid hit expansion by making use of EU-OPENSCREEN resources.
Authors: Benz, L.S. / Wollenhaupt, J. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.
History
DepositionJun 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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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)34,90810
Polymers33,8141
Non-polymers1,0949
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.300, 73.470, 52.530
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211

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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 , 7 types, 276 molecules

#2: Chemical ChemComp-A1CFT / 1-[5-(4-fluorophenyl)-1H-imidazol-2-yl]methanamine


Mass: 191.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10FN3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 29 % (w/v) PEG 4000, 0.1 M ammonium acetate and 0.1 M sodium acetate, pH 4.6
Time: 2-3 days

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.13→36.73 Å / Num. obs: 118199 / % possible obs: 96.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.09 / Net I/σ(I): 7.92 / Num. measured all: 397296
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
1.13-1.19911.56157505179570.3291.870.65
1.19-1.2896.21.05659317178200.4861.261.03
1.28-1.38970.66655705167480.6840.7951.64
1.38-1.5198.30.37253753156330.8720.4423.03
1.51-1.6997.80.19347049140730.960.235.6
1.69-1.9599.20.09544355125960.9910.11211.33
1.95-2.39980.05434933105590.9960.06419.62
2.39-3.3798.70.0362917982240.9980.04328.71

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→36.73 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1717 2099 1.78 %
Rwork0.1659 --
obs0.166 118151 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.13→36.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 74 267 2711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062593
X-RAY DIFFRACTIONf_angle_d0.9393563
X-RAY DIFFRACTIONf_dihedral_angle_d12.364871
X-RAY DIFFRACTIONf_chiral_restr0.077417
X-RAY DIFFRACTIONf_plane_restr0.007455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.150.38041230.36976747X-RAY DIFFRACTION85
1.15-1.180.33261370.33637564X-RAY DIFFRACTION95
1.18-1.210.31321380.30977670X-RAY DIFFRACTION96
1.21-1.250.30191400.29847700X-RAY DIFFRACTION96
1.25-1.290.27361390.27527692X-RAY DIFFRACTION96
1.29-1.340.26731390.24797670X-RAY DIFFRACTION97
1.34-1.390.21851410.22257842X-RAY DIFFRACTION98
1.39-1.450.19321410.20137835X-RAY DIFFRACTION98
1.45-1.530.20991430.17897883X-RAY DIFFRACTION99
1.53-1.620.17121410.15117785X-RAY DIFFRACTION97
1.62-1.750.13721430.13657916X-RAY DIFFRACTION99
1.75-1.930.13481430.12967912X-RAY DIFFRACTION99
1.93-2.210.13581430.12357916X-RAY DIFFRACTION99
2.21-2.780.15031440.13757911X-RAY DIFFRACTION98
2.78-36.730.14691440.14988009X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3113-0.0640.0120.46160.05330.9943-0.0221-0.05210.02630.0409-0.00660.0016-0.0003-0.03820.03030.11720.0007-0.01880.123700.119833.4255-5.947563.976
21.3935-0.19470.44870.5188-0.1440.4939-0.021-0.00570.03610.004-0.0263-0.0588-0.0355-0.00480.05410.1194-0.0015-0.00320.10790.00110.105830.08767.166544.6765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 183 )
2X-RAY DIFFRACTION2chain 'A' and (resid 184 through 330 )

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