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- PDB-8c6s: Fragment screening hit III bound to endothiapepsin -

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Basic information

Entry
Database: PDB / ID: 8c6s
TitleFragment screening hit III bound to endothiapepsin
ComponentsEndothiapepsin
KeywordsHYDROLASE / Fragment / Complex / Screening / Protease
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
4-(1,4-diazepan-1-ylsulfonyl)isoquinoline / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsWiese, J.N. / Buehrmann, M. / Mueller, M.P. / Rauh, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 212/474-1 FUGG Germany
CitationJournal: J.Med.Chem. / Year: 2023
Title: Fragtory: Pharmacophore-Focused Design, Synthesis, and Evaluation of an sp 3 -Enriched Fragment Library.
Authors: Buhrmann, M. / Kallepu, S. / Warmuth, J.D. / Wiese, J.N. / Ehrt, C. / Vatheuer, H. / Hiller, W. / Seitz, C. / Levy, L. / Czodrowski, P. / Sievers, S. / Muller, M.P. / Rauh, D.
History
DepositionJan 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)43,6623
Polymers43,2791
Non-polymers3832
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.390, 73.420, 53.200
Angle α, β, γ (deg.)90.000, 110.020, 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: 43278.664 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TUU / 4-(1,4-diazepan-1-ylsulfonyl)isoquinoline


Mass: 291.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 0.1 M ammonium acetate, 24 - 30 % PEG4000; microseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→36.88 Å / Num. obs: 124155 / % possible obs: 93.6 % / Redundancy: 6.18 % / Biso Wilson estimate: 11.71 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.098 / Net I/σ(I): 12.44
Reflection shellResolution: 1.1→1.2 Å / Num. unique obs: 124155 / CC1/2: 0.095

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→36.88 Å / SU ML: 0.0805 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 12.5149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1488 6208 5 %
Rwork0.1348 117947 -
obs0.1355 124155 93.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.89 Å2
Refinement stepCycle: LAST / Resolution: 1.1→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 26 494 2899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662553
X-RAY DIFFRACTIONf_angle_d1.00123531
X-RAY DIFFRACTIONf_chiral_restr0.0837425
X-RAY DIFFRACTIONf_plane_restr0.0072447
X-RAY DIFFRACTIONf_dihedral_angle_d11.0544855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.1711300.1422471X-RAY DIFFRACTION58.5
1.11-1.130.14681440.13242735X-RAY DIFFRACTION65.67
1.13-1.140.1631580.12013010X-RAY DIFFRACTION71.58
1.14-1.150.13271830.12263474X-RAY DIFFRACTION83.46
1.15-1.170.12972000.11333806X-RAY DIFFRACTION91.42
1.17-1.180.12122060.11563912X-RAY DIFFRACTION92.54
1.18-1.20.13742050.11553894X-RAY DIFFRACTION93.8
1.2-1.220.13742100.11773996X-RAY DIFFRACTION95.27
1.22-1.240.15332110.12034006X-RAY DIFFRACTION95.58
1.24-1.260.14572120.11484014X-RAY DIFFRACTION95.87
1.26-1.280.15422090.11833987X-RAY DIFFRACTION95.84
1.28-1.30.16032130.12084045X-RAY DIFFRACTION96.44
1.3-1.330.13252130.11564036X-RAY DIFFRACTION96.07
1.33-1.360.13592130.1214058X-RAY DIFFRACTION96.87
1.36-1.390.1422130.11454040X-RAY DIFFRACTION96.86
1.39-1.420.13642170.11534122X-RAY DIFFRACTION97.4
1.42-1.450.14022130.11994050X-RAY DIFFRACTION97.66
1.45-1.490.14222160.11984108X-RAY DIFFRACTION97.94
1.49-1.540.13762180.1184137X-RAY DIFFRACTION98.28
1.54-1.590.11522160.11554107X-RAY DIFFRACTION98.47
1.59-1.640.14422180.12144141X-RAY DIFFRACTION98.69
1.64-1.710.14912190.12664164X-RAY DIFFRACTION98.78
1.71-1.790.14862180.13454146X-RAY DIFFRACTION98.98
1.79-1.880.1272200.13654180X-RAY DIFFRACTION99.23
1.88-20.14392200.13094164X-RAY DIFFRACTION99.48
2-2.150.13752210.13054215X-RAY DIFFRACTION99.71
2.15-2.370.15272220.1414205X-RAY DIFFRACTION99.86
2.37-2.710.16432220.1534217X-RAY DIFFRACTION99.95
2.71-3.420.17142220.1524218X-RAY DIFFRACTION99.82
3.42-36.880.15292260.14464289X-RAY DIFFRACTION99.73

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