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- PDB-7if9: Crystal structure of Endothiapepsin in complex with fragment EOS1... -

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Basic information

Entry
Database: PDB / ID: 7if9
TitleCrystal structure of Endothiapepsin in complex with fragment EOS103056 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
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9512
Polymers33,8141
Non-polymers1371
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.360, 73.390, 52.590
Angle α, β, γ (deg.)90.00, 109.49, 90.00
Int Tables number4
Space group name H-MP1211

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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-A1CFY / 2-propylpyrimidin-4-amine


Mass: 137.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
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: 1.18→42.76 Å / Num. obs: 104617 / % possible obs: 97.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.072 / Net I/σ(I): 10.89 / Num. measured all: 349607
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
1.18-1.25930.85952498161330.541.0271.23
1.25-1.3397.20.62950991158150.6630.7541.69
1.33-1.4498.30.3951587148840.8680.4612.91
1.44-1.5898.50.22446235137630.9470.2664.97
1.58-1.7698.70.12842545124630.9820.1528.7
1.76-2.04990.06638125110470.9950.07816.77
2.04-2.4997.50.0422968692180.9970.0525.73
2.49-3.5298.60.0272470072490.9990.03336.46

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→42.76 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.824 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17126 2100 2 %RANDOM
Rwork0.16234 ---
obs0.16253 102514 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0 Å2-0.29 Å2
2--0.22 Å2-0 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.18→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 10 301 2680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0144228
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183541
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.6334940
X-RAY DIFFRACTIONr_angle_other_deg1.5921.5787017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8795536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94825.702121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.99415478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.951151
X-RAY DIFFRACTIONr_chiral_restr0.0880.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024484
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02786
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8911.2352345
X-RAY DIFFRACTIONr_mcbond_other0.8941.232316
X-RAY DIFFRACTIONr_mcangle_it1.4891.8162550
X-RAY DIFFRACTIONr_mcangle_other1.491.8162551
X-RAY DIFFRACTIONr_scbond_it1.2991.2931883
X-RAY DIFFRACTIONr_scbond_other1.2991.2931883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0231.8612391
X-RAY DIFFRACTIONr_long_range_B_refined3.8415.4274055
X-RAY DIFFRACTIONr_long_range_B_other3.55815.0013973
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.177→1.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 142 -
Rwork0.295 6932 -
obs--89.07 %

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