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- PDB-8q0y: Endothiapepsin in complex with ligand (3R,5R)-5-(3-(4-bromophenyl... -

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Basic information

Entry
Database: PDB / ID: 8q0y
TitleEndothiapepsin in complex with ligand (3R,5R)-5-(3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl)-3-(2-((methyl(prop-2-yn-1-yl)amino)methyl)thiazol-4-yl)pyrrolidin-3-ol (CBWS-SE-085.1)
ComponentsEndothiapepsin
KeywordsHYDROLASE / Endothiapepsin / ligand 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
ACETATE ION / : / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsMueller, J.M. / Eckelt, S. / Klebe, G. / Glinca, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structures of Endothiapepsin with ligands derived from merged fragment hits
Authors: Mueller, J.M.
History
DepositionJul 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: 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)34,8379
Polymers33,8141
Non-polymers1,0238
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-0 kcal/mol
Surface area12620 Å2
Unit cell
Length a, b, c (Å)44.855, 72.626, 52.432
Angle α, β, γ (deg.)90.000, 109.200, 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

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Protein , 1 types, 1 molecules A

#1: Protein Endothiapepsin / Aspartate protease


Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin

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Non-polymers , 5 types, 267 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-IJ9 / (3~{R},5~{R})-5-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]-3-[2-[[methyl(prop-2-ynyl)amino]methyl]-1,3-thiazol-4-yl]pyrrolidin-3-ol


Mass: 474.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20BrN5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein at 5 mg/mL in 100 mM ammoniumacetate pH 4.6, reservoir: 100 mM ammoniumacetate, 100 mM sodium acetate pH 4.6, 24 % PEG4000, 292 K, 2+2 yL drops over 1 mL reservoir, streak seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99187 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 89523 / % possible obs: 96.6 % / Redundancy: 3.82 % / Biso Wilson estimate: 12.38 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.17
Reflection shellResolution: 1.23→1.3 Å / Redundancy: 3.65 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 13414 / CC1/2: 0.947 / % possible all: 90.1

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→39.17 Å / SU ML: 0.0879 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.6363
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1519 4474 5 %
Rwork0.1323 85035 -
obs0.1333 89509 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.63 Å2
Refinement stepCycle: LAST / Resolution: 1.23→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 61 259 2687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642585
X-RAY DIFFRACTIONf_angle_d0.98993565
X-RAY DIFFRACTIONf_chiral_restr0.0825419
X-RAY DIFFRACTIONf_plane_restr0.0066459
X-RAY DIFFRACTIONf_dihedral_angle_d13.067833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.240.18351230.1572339X-RAY DIFFRACTION80.38
1.24-1.260.18791400.14192658X-RAY DIFFRACTION90.52
1.26-1.270.17541390.13242659X-RAY DIFFRACTION91.98
1.27-1.290.15371450.12432741X-RAY DIFFRACTION93.55
1.29-1.30.17631450.12082769X-RAY DIFFRACTION95.26
1.3-1.320.14751500.11662838X-RAY DIFFRACTION95.89
1.32-1.340.16431480.11392804X-RAY DIFFRACTION96.25
1.34-1.360.14161460.11242806X-RAY DIFFRACTION96.63
1.36-1.380.14171490.11182834X-RAY DIFFRACTION96.35
1.38-1.40.1531490.11322832X-RAY DIFFRACTION96.75
1.4-1.430.17821480.11622800X-RAY DIFFRACTION96.69
1.43-1.450.16461510.12082870X-RAY DIFFRACTION97.04
1.45-1.480.14091480.11932825X-RAY DIFFRACTION96.81
1.48-1.510.14881490.1162831X-RAY DIFFRACTION97.16
1.51-1.550.14961510.10742867X-RAY DIFFRACTION97.45
1.55-1.580.14781510.10082855X-RAY DIFFRACTION97.47
1.58-1.620.12621490.10162846X-RAY DIFFRACTION97.94
1.62-1.670.1361520.10242880X-RAY DIFFRACTION97.9
1.67-1.710.11341510.10652869X-RAY DIFFRACTION98.21
1.71-1.770.12221520.11042885X-RAY DIFFRACTION97.94
1.77-1.830.15291510.1162874X-RAY DIFFRACTION98.69
1.83-1.910.14361530.11962899X-RAY DIFFRACTION98.64
1.91-1.990.13751530.11352913X-RAY DIFFRACTION98.71
1.99-2.10.11561530.11232901X-RAY DIFFRACTION98.9
2.1-2.230.12941520.1172894X-RAY DIFFRACTION99.12
2.23-2.40.14761550.13112940X-RAY DIFFRACTION99.49
2.4-2.640.16491540.14682934X-RAY DIFFRACTION99.61
2.64-3.030.1651550.15312938X-RAY DIFFRACTION99.87
3.03-3.810.17451560.15482953X-RAY DIFFRACTION99.3
3.81-39.170.16351560.16232981X-RAY DIFFRACTION99.21

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