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- PDB-9rg6: Crystal structure of Endothiapepsin in complex with follow-up com... -

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Basic information

Entry
Database: PDB / ID: 9rg6
TitleCrystal structure of Endothiapepsin in complex with follow-up compound EOS97152 from ECBL
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: 1.07 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: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)34,1363
Polymers33,8141
Non-polymers3222
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.330, 72.760, 52.610
Angle α, β, γ (deg.)90.00, 109.33, 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-A1JFV / ~{N}-[3-(aminomethyl)phenyl]-4-fluoranyl-benzamide


Mass: 244.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13FN2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.07→49.65 Å / Num. obs: 132704 / % possible obs: 92.4 % / Redundancy: 4.32 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.092 / Net I/σ(I): 7.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.07-1.131.2960.94193500.4641.5031
1.13-1.210.805196000.6860.9181
1.21-1.30.583187640.8010.661
1.3-1.430.356176390.9070.4061
1.43-1.60.196160710.9690.2231
1.6-1.840.112143330.990.1261
1.84-2.260.071121640.9940.081
2.26-3.190.05494150.9950.0611
3.19-49.650.04853680.9960.0531

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→22.25 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.176 2099 1.58 %
Rwork0.1551 --
obs0.1554 132661 92.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.07→22.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 22 315 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062540
X-RAY DIFFRACTIONf_angle_d0.8953505
X-RAY DIFFRACTIONf_dihedral_angle_d6.648391
X-RAY DIFFRACTIONf_chiral_restr0.076416
X-RAY DIFFRACTIONf_plane_restr0.009458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.090.36181130.32067034X-RAY DIFFRACTION75
1.09-1.120.32681360.28868420X-RAY DIFFRACTION90
1.12-1.150.27341340.26488360X-RAY DIFFRACTION89
1.15-1.180.25451360.24298439X-RAY DIFFRACTION90
1.18-1.220.22071370.22268543X-RAY DIFFRACTION91
1.22-1.260.20671400.20798678X-RAY DIFFRACTION92
1.26-1.310.21271410.19698773X-RAY DIFFRACTION94
1.31-1.370.20531420.17938845X-RAY DIFFRACTION94
1.37-1.450.1721430.16658920X-RAY DIFFRACTION95
1.45-1.540.17851440.15028959X-RAY DIFFRACTION95
1.54-1.650.15471450.13729010X-RAY DIFFRACTION96
1.65-1.820.15091460.12699079X-RAY DIFFRACTION96
1.82-2.080.14731460.12459081X-RAY DIFFRACTION96
2.08-2.630.15191460.12859091X-RAY DIFFRACTION96
2.63-22.250.16781500.14569330X-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)
10.3091-0.048-0.01040.44220.05471.0874-0.0232-0.05120.03560.0356-0.00570.0017-0.0111-0.0410.03140.07690.0023-0.02740.1006-0.00160.124433.5328-5.991764.1104
21.073-0.1560.34450.6056-0.14620.6288-0.01370.00460.0341-0.0016-0.0224-0.0596-0.0266-0.00540.03970.0667-0.0012-0.01120.07110.00080.098630.17767.014444.7228
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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