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- PDB-5sap: Endothiapepsin in complex with compound FU58-2 -

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Basic information

Entry
Database: PDB / ID: 5sap
TitleEndothiapepsin in complex with compound FU58-2
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-ZSG / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.04 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

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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)43,9176
Polymers43,2791
Non-polymers6395
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.410, 73.490, 53.150
Angle α, β, γ (deg.)90.000, 110.147, 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-ZSG / (8S)-5-(2-aminopyrimidin-4-yl)-N-[2-(dimethylamino)ethyl]-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazine-2-carboxamide


Mass: 330.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 36.06 %
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: 1.04→42.63 Å / Num. obs: 152537 / % possible obs: 97.1 % / Redundancy: 3.764 % / Biso Wilson estimate: 13.604 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.086 / Χ2: 1.126 / Net I/σ(I): 8.24 / Num. measured all: 574223
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
1.04-1.13.7231.1790.878965025350240830.4111.37395
1.1-1.183.6960.6041.88435423796228210.7040.70495.9
1.18-1.273.7430.4142.698039322205214810.830.48396.7
1.27-1.393.770.283.997463320416197940.9160.32697
1.39-1.563.780.1616.956859418477181450.9710.18798.2
1.56-1.83.8340.09511.926169216324160920.9890.1198.6
1.8-2.23.7340.05919.845078113824135980.9940.06898.4
2.2-3.113.9190.04726.724161210714106180.9960.05499.1
3.11-42.633.8130.0431.6322514599459050.9960.04798.5

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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: 1.04→42.63 Å / SU ML: 0.1179 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.3537
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1487 2101 1.38 %
Rwork0.1338 150436 -
obs0.134 152537 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.29 Å2
Refinement stepCycle: LAST / Resolution: 1.04→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 44 394 2827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532679
X-RAY DIFFRACTIONf_angle_d0.91883694
X-RAY DIFFRACTIONf_chiral_restr0.0751429
X-RAY DIFFRACTIONf_plane_restr0.0064492
X-RAY DIFFRACTIONf_dihedral_angle_d7.0412425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.060.34451350.33919664X-RAY DIFFRACTION93.82
1.06-1.090.2971380.2889877X-RAY DIFFRACTION95.98
1.09-1.120.27151370.23939847X-RAY DIFFRACTION95.82
1.12-1.150.20781380.20389828X-RAY DIFFRACTION95.47
1.15-1.190.17951390.18179949X-RAY DIFFRACTION96.78
1.19-1.230.18511390.16819974X-RAY DIFFRACTION96.85
1.23-1.280.18151390.15319973X-RAY DIFFRACTION96.69
1.28-1.340.1421390.13469925X-RAY DIFFRACTION96.66
1.34-1.410.14041410.117710091X-RAY DIFFRACTION97.78
1.41-1.50.13061410.106710163X-RAY DIFFRACTION98.46
1.5-1.610.11581410.102410083X-RAY DIFFRACTION97.76
1.61-1.780.14091430.101210247X-RAY DIFFRACTION99.25
1.78-2.030.10881430.10510250X-RAY DIFFRACTION99.28
2.03-2.560.1491420.115510172X-RAY DIFFRACTION98.11
2.56-42.630.13561460.132910393X-RAY DIFFRACTION99.12

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