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- PDB-8c74: Pyrrolidine fragment 10d bound to endothiapepsin -

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Basic information

Entry
Database: PDB / ID: 8c74
TitlePyrrolidine fragment 10d 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
Chem-TWX / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 1.1Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9214
Polymers43,2791
Non-polymers6433
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.340, 72.820, 52.760
Angle α, β, γ (deg.)90.000, 109.230, 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-TWX / (3~{R},4~{R})-4-[4-[(4-azanylphenoxy)methyl]-1,2,3-triazol-1-yl]pyrrolidin-3-ol


Mass: 275.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 1.9 Å3/Da / Density % sol: 35.27 %
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

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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: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→42.81 Å / Num. obs: 108821 / % possible obs: 94.9 % / Redundancy: 6.16 % / Biso Wilson estimate: 13.07 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.044 / Net I/σ(I): 21.39
Reflection shellResolution: 1.15→1.25 Å / Num. unique obs: 20962 / CC1/2: 0.97

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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: 1.15→42.81 Å / SU ML: 0.0797 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 12.9529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1479 5441 5 %
Rwork0.1309 103380 -
obs0.1318 108821 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.16 Å2
Refinement stepCycle: LAST / Resolution: 1.15→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 46 524 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672557
X-RAY DIFFRACTIONf_angle_d0.97673526
X-RAY DIFFRACTIONf_chiral_restr0.0827420
X-RAY DIFFRACTIONf_plane_restr0.0065447
X-RAY DIFFRACTIONf_dihedral_angle_d10.8759846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.1651220.13682307X-RAY DIFFRACTION63.26
1.16-1.180.16441330.12852532X-RAY DIFFRACTION70.43
1.18-1.190.12771490.1232826X-RAY DIFFRACTION77.86
1.19-1.210.12241650.12163146X-RAY DIFFRACTION88.18
1.21-1.220.13881810.11843430X-RAY DIFFRACTION94.09
1.22-1.240.14441810.12343434X-RAY DIFFRACTION95.46
1.24-1.260.13811840.11373507X-RAY DIFFRACTION96.04
1.26-1.280.13481810.10883452X-RAY DIFFRACTION96.37
1.28-1.30.12931850.11073526X-RAY DIFFRACTION96.89
1.3-1.320.1431840.11453485X-RAY DIFFRACTION96.83
1.32-1.340.12321860.11353530X-RAY DIFFRACTION96.9
1.34-1.360.14821850.11463524X-RAY DIFFRACTION97.25
1.36-1.390.14851840.10333494X-RAY DIFFRACTION97.35
1.39-1.420.12581860.10563530X-RAY DIFFRACTION97.56
1.42-1.450.14381870.10293549X-RAY DIFFRACTION97.72
1.45-1.480.12861860.10563530X-RAY DIFFRACTION97.79
1.48-1.520.13931870.10843571X-RAY DIFFRACTION98.09
1.52-1.560.12911880.11183555X-RAY DIFFRACTION98.42
1.56-1.610.1341890.11263592X-RAY DIFFRACTION98.44
1.61-1.660.13841870.1183556X-RAY DIFFRACTION98.4
1.66-1.720.14891890.12193600X-RAY DIFFRACTION99.16
1.72-1.790.15121890.12783587X-RAY DIFFRACTION98.87
1.79-1.870.14691890.13173585X-RAY DIFFRACTION99.08
1.87-1.970.14371920.12863648X-RAY DIFFRACTION99.35
1.97-2.090.13041900.12333608X-RAY DIFFRACTION99.55
2.09-2.250.14481900.12443622X-RAY DIFFRACTION99.79
2.25-2.480.15971920.14333637X-RAY DIFFRACTION99.84
2.48-2.840.16591920.14973654X-RAY DIFFRACTION99.95
2.84-3.570.15951930.14683670X-RAY DIFFRACTION99.95
3.57-42.810.14941950.13993693X-RAY DIFFRACTION99.59

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