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

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Basic information

Entry
Database: PDB / ID: 7iew
TitleCrystal structure of Endothiapepsin in complex with fragment EOS102818 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
1-(quinolin-3-yl)methanamine / Endothiapepsin
Similarity search - Component
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)34,1303
Polymers33,8141
Non-polymers3162
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.410, 73.480, 52.680
Angle α, β, γ (deg.)90.00, 109.53, 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-WQY / 1-(quinolin-3-yl)methanamine


Mass: 158.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
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→39.62 Å / Num. obs: 105031 / % possible obs: 97.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.087 / Net I/σ(I): 7.88 / Num. measured all: 351007
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
1.18-1.2593.91.41853083163090.3391.6930.82
1.25-1.3396.70.92250609158080.5181.1061.25
1.33-1.4498.40.53351469149520.7770.632.26
1.44-1.5898.40.28546204138040.9180.344.06
1.58-1.7698.60.15342556124840.9740.1817.26
1.76-2.0499.10.08238305110970.9920.09713.15
2.04-2.4997.60.0553013192670.9950.06618.64
2.49-3.5298.20.0432500972440.9970.05124.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→39.62 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.954 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19781 2100 2 %RANDOM
Rwork0.17008 ---
obs0.17063 102930 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.284 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0.34 Å2
2--0.27 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.18→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 24 292 2685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0144278
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183563
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6434969
X-RAY DIFFRACTIONr_angle_other_deg1.5681.5797036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8575536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66725.478115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.62515475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.782151
X-RAY DIFFRACTIONr_chiral_restr0.0870.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024484
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02802
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_it0.9791.3572368
X-RAY DIFFRACTIONr_mcbond_other0.9831.3462341
X-RAY DIFFRACTIONr_mcangle_it1.6241.9942556
X-RAY DIFFRACTIONr_mcangle_other1.6241.9952557
X-RAY DIFFRACTIONr_scbond_it1.3351.4281910
X-RAY DIFFRACTIONr_scbond_other1.3341.4281911
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0782.0652414
X-RAY DIFFRACTIONr_long_range_B_refined4.07416.8654126
X-RAY DIFFRACTIONr_long_range_B_other3.70116.474051
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.18→1.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 143 -
Rwork0.344 7012 -
obs--90.19 %

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