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- PDB-8c72: Pyrrolidine fragment 10b bound to endothiapepsin -

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Basic information

Entry
Database: PDB / ID: 8c72
TitlePyrrolidine fragment 10b 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-TW0 / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 6, 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)43,8614
Polymers43,2791
Non-polymers5833
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 73.880, 53.130
Angle α, β, γ (deg.)90.000, 110.080, 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-TW0 / (3~{S},4~{S})-4-(4-pyridin-2-yl-1,2,3-triazol-1-yl)piperidin-3-ol


Mass: 245.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 1.93 Å3/Da / Density % sol: 36.39 %
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: 1.2→42.64 Å / Num. obs: 102507 / % possible obs: 99.7 % / Redundancy: 6.22 % / Biso Wilson estimate: 10.98 Å2 / CC1/2: 1 / Rrim(I) all: 0.029 / Net I/σ(I): 36.79
Reflection shellResolution: 1.2→1.3 Å / Num. unique obs: 21772 / CC1/2: 0.99

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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: 1.2→42.64 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 9.4823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1273 5126 5 %
Rwork0.1114 97381 -
obs0.1122 102507 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.71 Å2
Refinement stepCycle: LAST / Resolution: 1.2→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 42 565 2992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082657
X-RAY DIFFRACTIONf_angle_d1.06643679
X-RAY DIFFRACTIONf_chiral_restr0.0932442
X-RAY DIFFRACTIONf_plane_restr0.0073469
X-RAY DIFFRACTIONf_dihedral_angle_d10.5773907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.11971660.08513154X-RAY DIFFRACTION97.68
1.21-1.230.10661720.08333261X-RAY DIFFRACTION99.94
1.23-1.240.10151690.08393217X-RAY DIFFRACTION99.97
1.24-1.260.10781720.08183257X-RAY DIFFRACTION99.91
1.26-1.280.11561700.0843243X-RAY DIFFRACTION100
1.28-1.290.11721710.08523236X-RAY DIFFRACTION99.5
1.29-1.310.10511670.0873178X-RAY DIFFRACTION99.88
1.31-1.330.11051730.08723287X-RAY DIFFRACTION100
1.33-1.350.12121700.08893234X-RAY DIFFRACTION99.97
1.35-1.370.12271700.08673224X-RAY DIFFRACTION99.97
1.37-1.40.12131710.09553260X-RAY DIFFRACTION99.97
1.4-1.420.12261720.093269X-RAY DIFFRACTION99.94
1.42-1.450.121680.08843185X-RAY DIFFRACTION99.85
1.45-1.480.09951710.08313256X-RAY DIFFRACTION100
1.48-1.510.10841710.08283239X-RAY DIFFRACTION99.94
1.51-1.550.10911700.08113242X-RAY DIFFRACTION99.91
1.55-1.590.10821700.08313228X-RAY DIFFRACTION99.97
1.59-1.630.11631720.08793267X-RAY DIFFRACTION99.97
1.63-1.680.13211720.09323256X-RAY DIFFRACTION99.94
1.68-1.730.11231700.10273234X-RAY DIFFRACTION100
1.73-1.790.12931710.10783257X-RAY DIFFRACTION99.91
1.79-1.860.12871700.10793225X-RAY DIFFRACTION99.91
1.86-1.950.11171720.10783269X-RAY DIFFRACTION99.91
1.95-2.050.11461720.10363258X-RAY DIFFRACTION99.85
2.05-2.180.12041710.10943253X-RAY DIFFRACTION100
2.18-2.350.14481720.12033263X-RAY DIFFRACTION100
2.35-2.590.13241710.13153266X-RAY DIFFRACTION99.97
2.59-2.960.15211720.13633268X-RAY DIFFRACTION99.83
2.96-3.730.13461730.13123274X-RAY DIFFRACTION99.91
3.73-42.640.14111750.13093321X-RAY DIFFRACTION99.52

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