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- PDB-3q6y: Endothiapepsin in complex with a pyrrolidine based inhibitor -

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Basic information

Entry
Database: PDB / ID: 3q6y
TitleEndothiapepsin in complex with a pyrrolidine based inhibitor
ComponentsEndothiapepsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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-S47 / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.351 Å
AuthorsKoester, H. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Endothiapepsin in complex with a pyrrolidine based inhibitor
Authors: Koester, H. / Heine, A. / Klebe, G.
History
DepositionJan 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7546
Polymers33,8141
Non-polymers9405
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.360, 72.790, 51.790
Angle α, β, γ (deg.)90.00, 108.60, 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 , 5 types, 228 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-S47 / (3S,4S)-pyrrolidine-3,4-diyl bis(naphthalen-1-ylacetate)


Mass: 439.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H25NO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M NH4Ac, 0.1 M Acetate-Buffer pH 4.6, 26 % PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2009 / Details: mirrors
RadiationMonochromator: Bertels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. all: 68334 / Num. obs: 68334 / % possible obs: 100 % / Redundancy: 3.6 % / Rsym value: 0.041 / Net I/σ(I): 28.6
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2764 / Rsym value: 0.315 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OEW

1oew


Resolution: 1.351→37.017 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 16.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1838 3370 5.09 %RANDOM
Rwork0.1656 ---
obs0.1666 66233 94.93 %-
all-66233 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.917 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0285 Å20 Å2-0.5684 Å2
2---1.0859 Å2-0 Å2
3---0.0575 Å2
Refinement stepCycle: LAST / Resolution: 1.351→37.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 65 223 2482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052420
X-RAY DIFFRACTIONf_angle_d1.0793327
X-RAY DIFFRACTIONf_dihedral_angle_d14.033809
X-RAY DIFFRACTIONf_chiral_restr0.07389
X-RAY DIFFRACTIONf_plane_restr0.005412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3512-1.39950.24252390.21794861X-RAY DIFFRACTION73
1.3995-1.45560.19823090.18946014X-RAY DIFFRACTION91
1.4556-1.52180.19053580.1676205X-RAY DIFFRACTION95
1.5218-1.60210.18083400.15686350X-RAY DIFFRACTION97
1.6021-1.70240.17243610.15216420X-RAY DIFFRACTION97
1.7024-1.83390.18353420.14926541X-RAY DIFFRACTION99
1.8339-2.01840.1773880.14726524X-RAY DIFFRACTION99
2.0184-2.31040.15623190.14726630X-RAY DIFFRACTION100
2.3104-2.91070.18413710.16816611X-RAY DIFFRACTION100
2.9107-37.03060.19373430.17956707X-RAY DIFFRACTION99

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