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- PDB-5sat: Endothiapepsin in complex with compound FU66-1 -

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Basic information

Entry
Database: PDB / ID: 5sat
TitleEndothiapepsin in complex with compound FU66-1
ComponentsEndothiapepsin
KeywordsHYDROLASE/HYDROLASE inhibitor / Frag4Lead / fragment screening / hydrolase / inhibition / HYDROLASE-HYDROLASE inhibitor complex
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-ZSY / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsWollenhaupt, J. / Metz, A. / Messini, N. / Barthel, T. / Klebe, G. / Weiss, M.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
BMBFFrag2Xtal 05K13RM1 and Frag4Lead 05K16RM1 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking.
Authors: Metz, A. / Wollenhaupt, J. / Glockner, S. / Messini, N. / Huber, S. / Barthel, T. / Merabet, A. / Gerber, H.D. / Heine, A. / Klebe, G. / Weiss, M.S.
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 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)43,7063
Polymers43,2791
Non-polymers4272
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.170, 73.400, 52.560
Angle α, β, γ (deg.)90.000, 109.369, 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-ZSY / N-cyclopropyl-6-(furan-2-yl)-2-hydroxy-N-[(pyridin-2-yl)methyl]pyridine-3-carboxamide


Mass: 335.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 35.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M NaAc pH 4.6, 0.1 M NH4Ac pH 7.0, 27% (w/v) PEG 4000, 1.5µL protein + 1.5µL reservoir + 0.1µL seeds
Seeding: seeds obtained from crystals of same condition using 24-33% PEG 4000, diluted to 1:15 -1:45

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→49.59 Å / Num. obs: 62630 / % possible obs: 98 % / Redundancy: 3.395 % / Biso Wilson estimate: 23.147 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.095 / Χ2: 1.004 / Net I/σ(I): 9.84 / Num. measured all: 212653
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.483.3411.5790.723349610308100250.3091.87797.3
1.48-1.593.280.9811.1730823969693960.5221.16996.9
1.59-1.713.4830.612.0330890900588690.7330.71998.5
1.71-1.883.3930.3223.7827809833481970.9070.38298.4
1.88-2.13.3920.1448.0724952749273570.9780.17198.2
2.1-2.423.5150.08213.8723136663365820.9920.09799.2
2.42-2.963.3180.05420.3418085562154500.9960.06497
2.96-4.183.5190.02738.615261438043370.9990.03299
4.18-49.593.3930.0249.748201246424170.9990.02498.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→49.59 Å / SU ML: 0.1944 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2054 3132 5 %
Rwork0.1607 59494 -
obs0.163 62626 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 31 197 2617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142634
X-RAY DIFFRACTIONf_angle_d1.28363632
X-RAY DIFFRACTIONf_chiral_restr0.0954426
X-RAY DIFFRACTIONf_plane_restr0.0093487
X-RAY DIFFRACTIONf_dihedral_angle_d6.4837412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.33151410.31042686X-RAY DIFFRACTION95.64
1.42-1.440.37121400.30382641X-RAY DIFFRACTION97.99
1.44-1.470.34381420.29242704X-RAY DIFFRACTION97.9
1.47-1.50.32271410.28022688X-RAY DIFFRACTION97.55
1.5-1.520.32861380.27272622X-RAY DIFFRACTION96.37
1.52-1.560.29821400.24812653X-RAY DIFFRACTION96.61
1.56-1.590.29731420.21262692X-RAY DIFFRACTION98.1
1.59-1.630.25641440.19442743X-RAY DIFFRACTION98.77
1.63-1.670.23551420.1782705X-RAY DIFFRACTION98.48
1.67-1.710.26041420.17552687X-RAY DIFFRACTION98.61
1.71-1.760.23141430.16432712X-RAY DIFFRACTION98.69
1.76-1.820.21381430.15332724X-RAY DIFFRACTION98.56
1.82-1.880.23821420.14892703X-RAY DIFFRACTION97.6
1.88-1.960.20871410.13082675X-RAY DIFFRACTION97.1
1.96-2.050.17341450.11862748X-RAY DIFFRACTION99.52
2.05-2.160.15621430.11822723X-RAY DIFFRACTION99.38
2.16-2.290.1551440.12182737X-RAY DIFFRACTION99.41
2.29-2.470.18441430.13642725X-RAY DIFFRACTION99.27
2.47-2.720.2081420.14922680X-RAY DIFFRACTION96.84
2.72-3.110.17281410.15252693X-RAY DIFFRACTION97.52
3.11-3.920.19091460.15492761X-RAY DIFFRACTION99.45
3.92-49.590.18611470.1592792X-RAY DIFFRACTION98.36

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