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- PDB-3wz8: Endothiapepsin in complex with Gewald reaction-derived inhibitor (8) -

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Basic information

Entry
Database: PDB / ID: 3wz8
TitleEndothiapepsin in complex with Gewald reaction-derived inhibitor (8)
ComponentsEndothiapepsin
KeywordsHydrolase/Hydrolase inhibitor / aspartic protease / 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. / 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-IXV / DI(HYDROXYETHYL)ETHER / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKuhnert, M. / Steuber, H. / Diederich, W.E.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors
Authors: Kuhnert, M. / Koster, H. / Bartholomaus, R. / Park, A.Y. / Shahim, A. / Heine, A. / Steuber, H. / Klebe, G. / Diederich, W.E.
History
DepositionSep 19, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4544
Polymers33,8141
Non-polymers6403
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.610, 73.930, 54.190
Angle α, β, γ (deg.)90.00, 110.73, 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-IXV / N-benzyl-4-phenyl-2-[(N-phenyl-beta-alanyl)amino]thiophene-3-carboxamide


Mass: 455.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H25N3O2S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: ammonium acetate, PEG4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2013
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 59674 / Num. obs: 59674 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.65 Å2
Reflection shellResolution: 1.45→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.6 / Num. unique all: 15187 / Rsym value: 0.567 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OEW

1oew


Resolution: 1.45→40.442 Å / FOM work R set: 0.829 / SU ML: 0.18 / σ(F): 0 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 1770 3 %RANDOM
Rwork0.1887 ---
all0.1898 59066 --
obs0.1898 59066 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.74 Å2 / Biso mean: 10.69 Å2 / Biso min: 1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.45→40.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 44 566 2999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042537
X-RAY DIFFRACTIONf_angle_d0.9633479
X-RAY DIFFRACTIONf_chiral_restr0.058409
X-RAY DIFFRACTIONf_plane_restr0.004441
X-RAY DIFFRACTIONf_dihedral_angle_d13.323843
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.48920.36441340.32354331446598
1.4892-1.5330.2631370.262344194556100
1.533-1.58250.27721380.223744444582100
1.5825-1.63910.22461380.205644594597100
1.6391-1.70470.21071350.194243804515100
1.7047-1.78230.23011370.192844214558100
1.7823-1.87630.24531370.198144484585100
1.8763-1.99380.30071340.25334323445797
1.9938-2.14780.1981370.168644004537100
2.1478-2.36390.24631280.19874252438095
2.3639-2.70590.19151370.161444524589100
2.7059-3.40890.20421380.15544634601100
3.4089-40.45810.1831400.15554504464499

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