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- PDB-8q13: Endothiapepsin in complex with ligand (3R,5R)-5-(3-(2-amino-4-(tr... -

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Basic information

Entry
Database: PDB / ID: 8q13
TitleEndothiapepsin in complex with ligand (3R,5R)-5-(3-(2-amino-4-(trifluoromethyl)phenyl)-1,2,4-oxadiazol-5-yl)-3-(2-((methyl(prop-2-yn-1-yl)amino)methyl)thiazol-4-yl)pyrrolidin-3-ol (CBWS-SE-168)
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
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 6, 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)35,03810
Polymers33,8141
Non-polymers1,2249
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-13 kcal/mol
Surface area12480 Å2
Unit cell
Length a, b, c (Å)44.875, 72.688, 52.502
Angle α, β, γ (deg.)90.000, 109.240, 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: 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
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-IK5 / (3~{R},5~{R})-5-[3-[2-azanyl-4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]-3-[2-[[methyl(prop-2-ynyl)amino]methyl]-1,3-thiazol-4-yl]pyrrolidin-3-ol


Mass: 478.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21F3N6O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
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: PETRA III, DESY / Beamline: P11 / Wavelength: 0.688813 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688813 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 83863 / % possible obs: 98.3 % / Redundancy: 3.55 % / Biso Wilson estimate: 13.04 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.89
Reflection shellResolution: 1.26→1.34 Å / Redundancy: 3.47 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 13570 / CC1/2: 0.608 / % possible all: 98.7

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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: 1.26→36.6 Å / SU ML: 0.1336 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1761 4193 5 %
Rwork0.1466 79659 -
obs0.1481 83852 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.06 Å2
Refinement stepCycle: LAST / Resolution: 1.26→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 77 310 2757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392546
X-RAY DIFFRACTIONf_angle_d0.773504
X-RAY DIFFRACTIONf_chiral_restr0.0723412
X-RAY DIFFRACTIONf_plane_restr0.0048441
X-RAY DIFFRACTIONf_dihedral_angle_d15.5487818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.280.33831410.29442667X-RAY DIFFRACTION98.42
1.28-1.290.33191390.27492641X-RAY DIFFRACTION98.9
1.29-1.310.29031400.26322656X-RAY DIFFRACTION99.08
1.31-1.320.2521410.23832682X-RAY DIFFRACTION98.78
1.32-1.340.25021390.23072649X-RAY DIFFRACTION98.55
1.34-1.360.25271410.22482673X-RAY DIFFRACTION98.84
1.36-1.380.24131390.212643X-RAY DIFFRACTION97.79
1.38-1.40.27061330.20692533X-RAY DIFFRACTION94.44
1.4-1.420.23821290.19242440X-RAY DIFFRACTION91.1
1.42-1.450.23781400.18162667X-RAY DIFFRACTION98.77
1.45-1.470.18971400.16882645X-RAY DIFFRACTION99.5
1.47-1.50.2261430.15962723X-RAY DIFFRACTION99.27
1.5-1.530.22021370.15092605X-RAY DIFFRACTION99.31
1.53-1.560.1691420.13912705X-RAY DIFFRACTION99.27
1.56-1.590.18621410.12932668X-RAY DIFFRACTION99.19
1.59-1.630.17361400.11732669X-RAY DIFFRACTION99.33
1.63-1.670.14031410.11522676X-RAY DIFFRACTION99.3
1.67-1.710.15581420.11342698X-RAY DIFFRACTION99.72
1.71-1.760.17051410.11862670X-RAY DIFFRACTION99.5
1.76-1.820.16031420.12592695X-RAY DIFFRACTION99.33
1.82-1.890.16771410.12792687X-RAY DIFFRACTION99.51
1.89-1.960.13651410.11692678X-RAY DIFFRACTION99.12
1.96-2.050.13891400.12282667X-RAY DIFFRACTION99.01
2.05-2.160.16611410.12132675X-RAY DIFFRACTION99.12
2.16-2.290.15541410.13252666X-RAY DIFFRACTION98.6
2.29-2.470.16481400.14312664X-RAY DIFFRACTION98.42
2.47-2.720.18821290.14612447X-RAY DIFFRACTION90.23
2.72-3.110.17131420.15252706X-RAY DIFFRACTION99.41
3.11-3.920.17231420.14252705X-RAY DIFFRACTION99.58
3.92-36.60.1491450.14362759X-RAY DIFFRACTION99.18

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