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- PDB-5dq4: Endothiapepsin in complex with fragment 66 -

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Basic information

Entry
Database: PDB / ID: 5dq4
TitleEndothiapepsin in complex with fragment 66
ComponentsEndothiapepsin
KeywordsHYDROLASE / fragment screening / 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
1-[6-(furan-2-yl)pyridin-3-yl]methanamine / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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
DepositionSep 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: 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

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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)34,0803
Polymers33,8141
Non-polymers2662
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.128, 72.766, 52.596
Angle α, β, γ (deg.)90.00, 109.65, 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 / Fragment: UNP residues 90-419 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-5HQ / 1-[6-(furan-2-yl)pyridin-3-yl]methanamine


Mass: 174.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.86 %
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: BESSY / Beamline: 14.3 / Wavelength: 0.8912 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8912 Å / Relative weight: 1
ReflectionResolution: 1.15→42.5 Å / Num. obs: 111456 / % possible obs: 98.2 % / Redundancy: 4.07 % / Rsym value: 0.039 / Net I/σ(I): 21.36
Reflection shellResolution: 1.15→1.22 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 5.14 / % possible all: 91.8

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Processing

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

3pcw


Resolution: 1.15→16.511 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 9.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1299 5553 4.99 %
Rwork0.1105 --
obs0.1115 111393 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→16.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 19 339 2728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082595
X-RAY DIFFRACTIONf_angle_d1.2823581
X-RAY DIFFRACTIONf_dihedral_angle_d10.786860
X-RAY DIFFRACTIONf_chiral_restr0.07420
X-RAY DIFFRACTIONf_plane_restr0.007481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.1630.28911190.25222311X-RAY DIFFRACTION65
1.163-1.17660.151940.13683500X-RAY DIFFRACTION98
1.1766-1.1910.11611580.10923598X-RAY DIFFRACTION99
1.191-1.2060.11622000.10583521X-RAY DIFFRACTION99
1.206-1.22190.1241870.10193541X-RAY DIFFRACTION99
1.2219-1.23860.12891950.10233524X-RAY DIFFRACTION99
1.2386-1.25630.12811900.09913588X-RAY DIFFRACTION99
1.2563-1.27510.11951910.09853522X-RAY DIFFRACTION100
1.2751-1.2950.1152180.09993532X-RAY DIFFRACTION99
1.295-1.31620.12621700.09613610X-RAY DIFFRACTION99
1.3162-1.33890.11881970.09543538X-RAY DIFFRACTION100
1.3389-1.36320.11231810.09253558X-RAY DIFFRACTION100
1.3632-1.38950.12241680.08983599X-RAY DIFFRACTION100
1.3895-1.41780.11921770.08853618X-RAY DIFFRACTION100
1.4178-1.44860.10321850.08243551X-RAY DIFFRACTION100
1.4486-1.48230.10131900.08163586X-RAY DIFFRACTION100
1.4823-1.51930.10581870.08383556X-RAY DIFFRACTION100
1.5193-1.56040.10891890.08213600X-RAY DIFFRACTION100
1.5604-1.60630.10351880.0863581X-RAY DIFFRACTION100
1.6063-1.65810.11541880.0873577X-RAY DIFFRACTION100
1.6581-1.71730.11371880.09253573X-RAY DIFFRACTION100
1.7173-1.78590.11781880.09433579X-RAY DIFFRACTION100
1.7859-1.86710.10091900.09683613X-RAY DIFFRACTION100
1.8671-1.96540.09131880.09383592X-RAY DIFFRACTION100
1.9654-2.08830.11961890.09833588X-RAY DIFFRACTION100
2.0883-2.24920.10511890.10063588X-RAY DIFFRACTION100
2.2492-2.47490.11811880.1113592X-RAY DIFFRACTION100
2.4749-2.83140.13731910.12393621X-RAY DIFFRACTION100
2.8314-3.56140.15641900.13113614X-RAY DIFFRACTION100
3.5614-16.51270.19011800.15553469X-RAY DIFFRACTION94

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