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- PDB-3wz6: Endothiapepsin in complex with Gewald reaction-derived inhibitor (5) -

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Basic information

Entry
Database: PDB / ID: 3wz6
TitleEndothiapepsin in complex with Gewald reaction-derived inhibitor (5)
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
ACETATE ION / Chem-IXZ / DI(HYDROXYETHYL)ETHER / Chem-PG6 / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.404 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 1.1May 30, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 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 1.3Nov 13, 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)35,31410
Polymers33,8141
Non-polymers1,5009
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.420, 72.990, 53.180
Angle α, β, γ (deg.)90.00, 110.09, 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 , 6 types, 623 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-IXZ / N-benzyl-2-[(N-benzylglycyl)amino]-4-phenylthiophene-3-carboxamide


Mass: 455.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H25N3O2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 62145 / Num. obs: 62145 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.61 Å2
Reflection shellResolution: 1.4→1.6 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 3 / Num. unique all: 19124 / Rsym value: 0.646 / % possible all: 93.2

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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: 1.404→42.657 Å / FOM work R set: 0.9058 / SU ML: 0.13 / σ(F): 0 / Phase error: 16.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1633 1242 2 %RANDOM
Rwork0.1426 ---
all0.143 62136 --
obs0.143 62136 97.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.91 Å2 / Biso mean: 13.12 Å2 / Biso min: 2.94 Å2
Refinement stepCycle: LAST / Resolution: 1.404→42.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 103 614 3102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052639
X-RAY DIFFRACTIONf_angle_d1.0893609
X-RAY DIFFRACTIONf_chiral_restr0.063420
X-RAY DIFFRACTIONf_plane_restr0.005457
X-RAY DIFFRACTIONf_dihedral_angle_d13.035919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4039-1.46010.27761130.2585546565981
1.4601-1.52660.23951400.206968807020100
1.5266-1.60710.22121410.183668787019100
1.6071-1.70780.18751400.166269007040100
1.7078-1.83960.17781410.149769057046100
1.8396-2.02480.16631410.134668967037100
2.0248-2.31770.13411420.121169487090100
2.3177-2.920.15491410.124969277068100
2.92-42.67660.13291430.12470147157100

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