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- PDB-5sao: Endothiapepsin in complex with compound FU58-1 -

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Basic information

Entry
Database: PDB / ID: 5sao
TitleEndothiapepsin in complex with compound FU58-1
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-ZSD / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1 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)43,8635
Polymers43,2791
Non-polymers5854
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.310, 72.910, 52.620
Angle α, β, γ (deg.)90.000, 109.778, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZSD / 6-[(8R)-2-({[(3,5-dimethyl-1,2-oxazol-4-yl)methyl](methyl)amino}methyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl]pyrimidin-4-amine


Mass: 368.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N8O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 1.89 Å3/Da / Density % sol: 34.91 %
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→42.64 Å / Num. obs: 158879 / % possible obs: 91.6 % / Redundancy: 3.847 % / Biso Wilson estimate: 13.871 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.047 / Χ2: 1.102 / Net I/σ(I): 13.59 / Num. measured all: 611157
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
1-1.063.6891.0131.058060028009218470.5821.17978
1.06-1.133.8090.5052.239132826339239790.8560.58691
1.13-1.223.9590.274.239042124480228380.950.31293.3
1.22-1.343.8160.1885.938003822535209730.9720.21893.1
1.34-1.53.9640.11110.437699620405194230.9890.12995.2
1.5-1.733.8530.06418.376617118036171740.9960.07495.2
1.73-2.123.8570.03632.525697415241147720.9980.04296.9
2.12-2.993.8350.02645.024398411863114690.9990.0396.7
2.99-42.643.8480.02254.1924645660564040.9990.02697

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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→42.64 Å / SU ML: 0.111 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.8766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1458 2101 1.32 %
Rwork0.1313 156756 -
obs0.1315 158857 91.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.33 Å2
Refinement stepCycle: LAST / Resolution: 1→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 41 341 2771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542621
X-RAY DIFFRACTIONf_angle_d0.91463612
X-RAY DIFFRACTIONf_chiral_restr0.0755424
X-RAY DIFFRACTIONf_plane_restr0.0066482
X-RAY DIFFRACTIONf_dihedral_angle_d7.0209414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.020.3764970.3687204X-RAY DIFFRACTION63.27
1.02-1.050.30131330.30089919X-RAY DIFFRACTION87.09
1.05-1.080.22531390.236510384X-RAY DIFFRACTION91.49
1.08-1.110.18891400.190210483X-RAY DIFFRACTION92
1.11-1.140.1871380.158610273X-RAY DIFFRACTION90.4
1.14-1.190.16351420.139210576X-RAY DIFFRACTION93.16
1.19-1.230.14961430.129410679X-RAY DIFFRACTION93.66
1.23-1.290.131410.123310558X-RAY DIFFRACTION93.03
1.29-1.360.12631430.111310685X-RAY DIFFRACTION93.57
1.36-1.440.13881450.104110808X-RAY DIFFRACTION95.12
1.44-1.550.14321460.105710897X-RAY DIFFRACTION95.41
1.55-1.710.12431460.10510870X-RAY DIFFRACTION95.22
1.71-1.960.12671490.109311117X-RAY DIFFRACTION97.1
1.96-2.460.13261470.115910976X-RAY DIFFRACTION96.08
2.46-42.640.14461520.13911327X-RAY DIFFRACTION97.78

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