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- PDB-5isk: Endothiapepsin in complex with fluorinated primary amine fragment -

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Basic information

Entry
Database: PDB / ID: 5isk
TitleEndothiapepsin in complex with fluorinated primary amine fragment
ComponentsEndothiapepsin
KeywordsHYDROLASE / fragment screening / aspartic protease / inhibition
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
2-amino-1-(4-fluorophenyl)ethan-1-one / ACETATE ION / TRIETHYLENE GLYCOL / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsRadeva, N. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
BMBF05K13RM1 Germany
Citation
Journal: to be published
Title: Crystallographic Fragment Screening of an Entire Library
Authors: Radeva, N. / Heine, A. / Klebe, G.
#1: Journal: J. Med. Chem. / Year: 2011
Title: A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes.
Authors: Koester, H. / Craan, T. / Brass, S. / Herhaus, C. / Zentgraf, M. / Neumann, L. / Heine, A. / Klebe, G.
History
DepositionMar 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)34,75610
Polymers33,8141
Non-polymers9429
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint15 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.133, 72.870, 52.718
Angle α, β, γ (deg.)90.00, 109.28, 90.00
Int Tables number4
Space group name H-MP1211

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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 , 7 types, 352 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-6LZ / 2-amino-1-(4-fluorophenyl)ethan-1-one


Mass: 153.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8FNO
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.89 Å3/Da / Density % sol: 34.95 %
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
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→42.6 Å / Num. obs: 116418 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rsym value: 0.033 / Net I/σ(I): 16.8
Reflection shellResolution: 1.14→1.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.54 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1492refinement
Cootmodel building
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCW

3pcw


Resolution: 1.14→42.602 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1457 5814 5 %
Rwork0.1195 --
obs0.1208 116378 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.14→42.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 60 343 2775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072612
X-RAY DIFFRACTIONf_angle_d1.2283583
X-RAY DIFFRACTIONf_dihedral_angle_d10.572865
X-RAY DIFFRACTIONf_chiral_restr0.068417
X-RAY DIFFRACTIONf_plane_restr0.006471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1404-1.15340.2141870.21233565X-RAY DIFFRACTION97
1.1534-1.1670.22951940.19793667X-RAY DIFFRACTION100
1.167-1.18120.22711920.18573649X-RAY DIFFRACTION100
1.1812-1.19610.18771950.1743708X-RAY DIFFRACTION100
1.1961-1.21190.16971930.16343679X-RAY DIFFRACTION100
1.2119-1.22850.1951950.16113686X-RAY DIFFRACTION100
1.2285-1.2460.15651910.14823661X-RAY DIFFRACTION100
1.246-1.26460.16251940.14073686X-RAY DIFFRACTION100
1.2646-1.28440.1421950.13673698X-RAY DIFFRACTION100
1.2844-1.30550.16191920.12943657X-RAY DIFFRACTION100
1.3055-1.3280.16211950.12413694X-RAY DIFFRACTION100
1.328-1.35210.1331930.12213662X-RAY DIFFRACTION99
1.3521-1.37810.14441940.11973686X-RAY DIFFRACTION99
1.3781-1.40630.16611920.10933661X-RAY DIFFRACTION100
1.4063-1.43680.12741920.10753646X-RAY DIFFRACTION100
1.4368-1.47030.10981960.09713711X-RAY DIFFRACTION100
1.4703-1.5070.1131950.09643706X-RAY DIFFRACTION100
1.507-1.54780.12061940.08833684X-RAY DIFFRACTION100
1.5478-1.59330.10361940.08543684X-RAY DIFFRACTION100
1.5933-1.64480.10091930.08543680X-RAY DIFFRACTION100
1.6448-1.70360.121950.08883688X-RAY DIFFRACTION100
1.7036-1.77180.1241950.09093707X-RAY DIFFRACTION100
1.7718-1.85240.11921930.09393688X-RAY DIFFRACTION100
1.8524-1.95010.11751950.09543700X-RAY DIFFRACTION100
1.9501-2.07220.10811940.09223697X-RAY DIFFRACTION100
2.0722-2.23220.1211940.0963698X-RAY DIFFRACTION100
2.2322-2.45680.12881950.10973705X-RAY DIFFRACTION99
2.4568-2.81230.161940.1213713X-RAY DIFFRACTION100
2.8123-3.54290.1531950.13063726X-RAY DIFFRACTION100
3.5429-42.63120.18941980.15063772X-RAY DIFFRACTION99

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