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- PDB-6ron: Endothiapepsin in complex with compound 046 -

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Basic information

Entry
Database: PDB / ID: 6ron
TitleEndothiapepsin in complex with compound 046
ComponentsEndothiapepsin
KeywordsHYDROLASE / Aspartic Proteinase / Endothiapepsin / Complex with tetrazole / Inhibitor
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. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-KCE / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Endothiapepsin in complex with compound 046
Authors: Magari, F. / Heine, A. / Konstantinidou, M. / Sutanto, F. / Haupenthal, J. / Jumde, R.V. / Unver, M.Y. / Camacho, C.J. / Hirsch, A.K.H. / Doemling, A. / Klebe, G.
History
DepositionMay 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release

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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)34,4855
Polymers33,8141
Non-polymers6714
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint5 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.764, 73.352, 53.175
Angle α, β, γ (deg.)90.00, 109.65, 90.00
Int Tables number4
Space group name H-MP1211

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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-KCE / [(1~{S},2~{R})-1-[1-(1,3-benzodioxol-5-ylmethyl)-1,2,3,4-tetrazol-5-yl]-3-(4-~{tert}-butylphenyl)-2-methyl-propyl]diazane


Mass: 422.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystals obtained by streak-seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.13→43.1 Å / Num. obs: 122038 / % possible obs: 97.7 % / Redundancy: 5.1 % / CC1/2: 0.998 / Rsym value: 0.043 / Net I/σ(I): 15.8
Reflection shellResolution: 1.13→1.19 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 18907 / CC1/2: 0.87 / Rsym value: 0.483 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MxCuBEdata collection
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→43.1 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 12.81
RfactorNum. reflection% reflection
Rfree0.1527 5755 5 %
Rwork0.1343 --
obs0.1352 115124 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.15→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 45 330 2744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082548
X-RAY DIFFRACTIONf_angle_d0.9823510
X-RAY DIFFRACTIONf_dihedral_angle_d10.38850
X-RAY DIFFRACTIONf_chiral_restr0.083414
X-RAY DIFFRACTIONf_plane_restr0.007471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.16310.35731900.3633622X-RAY DIFFRACTION97
1.1631-1.17680.27021870.26993554X-RAY DIFFRACTION97
1.1768-1.19110.23641870.20463555X-RAY DIFFRACTION96
1.1911-1.20620.20541880.17313565X-RAY DIFFRACTION97
1.2062-1.22210.17381870.15293560X-RAY DIFFRACTION96
1.2221-1.23880.14711920.14083665X-RAY DIFFRACTION99
1.2388-1.25650.16351910.14163632X-RAY DIFFRACTION99
1.2565-1.27530.17771930.15513664X-RAY DIFFRACTION98
1.2753-1.29520.17661910.14683639X-RAY DIFFRACTION99
1.2952-1.31640.15381920.11413645X-RAY DIFFRACTION99
1.3164-1.33910.14021940.10843681X-RAY DIFFRACTION99
1.3391-1.36350.1241930.10693663X-RAY DIFFRACTION99
1.3635-1.38970.13491910.10593643X-RAY DIFFRACTION99
1.3897-1.41810.12791930.10673662X-RAY DIFFRACTION98
1.4181-1.44890.13141910.10513615X-RAY DIFFRACTION99
1.4489-1.48260.12991910.10223630X-RAY DIFFRACTION97
1.4826-1.51970.14491930.10623684X-RAY DIFFRACTION99
1.5197-1.56080.1241940.10453678X-RAY DIFFRACTION99
1.5608-1.60670.11631920.10423644X-RAY DIFFRACTION99
1.6067-1.65860.11911930.10563674X-RAY DIFFRACTION99
1.6586-1.71790.11721920.11113641X-RAY DIFFRACTION99
1.7179-1.78660.14671930.11523661X-RAY DIFFRACTION98
1.7866-1.8680.1361890.11953596X-RAY DIFFRACTION98
1.868-1.96640.14211930.11923673X-RAY DIFFRACTION98
1.9664-2.08960.14221900.1213606X-RAY DIFFRACTION97
2.0896-2.2510.13771930.12223678X-RAY DIFFRACTION99
2.251-2.47750.16491960.1333714X-RAY DIFFRACTION99
2.4775-2.83590.14241950.14363710X-RAY DIFFRACTION99
2.8359-3.57270.16521940.14683686X-RAY DIFFRACTION98
3.5727-43.13030.17641970.16233729X-RAY DIFFRACTION98

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