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- PDB-3pww: Endothiapepsin in complex with saquinavir -

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Basic information

Entry
Database: PDB / ID: 3pww
TitleEndothiapepsin in complex with saquinavir
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
Saquinavir / Chem-ROC / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsKoester, H. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2012
Title: Experimental and computational active site mapping as a starting point to fragment-based lead discovery.
Authors: Behnen, J. / Koster, H. / Neudert, G. / Craan, T. / Heine, A. / Klebe, G.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)34,5773
Polymers33,8141
Non-polymers7632
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.436, 73.039, 52.920
Angle α, β, γ (deg.)90.00, 109.71, 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-ROC / (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide / Fortovase / SAQUINAVIR / RO 31-8959


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 670.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H50N6O5 / References: Saquinavir / Comment: medication, antiretroviral*YM
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M NH4Ac, 0.1M Acetate-Buffer pH 4.6, 26% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 5, 2009 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.22→30 Å / Num. all: 94163 / Num. obs: 94163 / % possible obs: 100 % / Redundancy: 2.3 % / Rsym value: 0.049 / Net I/σ(I): 16.7
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3980 / Rsym value: 0.332 / % 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: 1.22→27.774 Å / SU ML: 0.11 / σ(F): 0 / Phase error: 15.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1781 1859 2.06 %RANDOM
Rwork0.1624 ---
obs0.1627 90280 93.51 %-
all-90280 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.775 Å2 / ksol: 0.447 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8946 Å20 Å2-0.9145 Å2
2--0.5087 Å2-0 Å2
3---0.3859 Å2
Refinement stepCycle: LAST / Resolution: 1.22→27.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 55 447 2871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052512
X-RAY DIFFRACTIONf_angle_d1.1353455
X-RAY DIFFRACTIONf_dihedral_angle_d13.137854
X-RAY DIFFRACTIONf_chiral_restr0.07413
X-RAY DIFFRACTIONf_plane_restr0.005437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.26360.24091550.21577535X-RAY DIFFRACTION79
1.2636-1.31420.20781640.19518276X-RAY DIFFRACTION89
1.3142-1.3740.19421880.17728527X-RAY DIFFRACTION90
1.374-1.44640.18171810.15928775X-RAY DIFFRACTION93
1.4464-1.53710.15911860.1498989X-RAY DIFFRACTION95
1.5371-1.65570.14971940.14639145X-RAY DIFFRACTION97
1.6557-1.82230.17431980.1489260X-RAY DIFFRACTION98
1.8223-2.08590.15521980.15179319X-RAY DIFFRACTION99
2.0859-2.62770.19122000.16229448X-RAY DIFFRACTION100
2.6277-27.7810.17871950.16619147X-RAY DIFFRACTION95

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