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- PDB-4y47: Endothiapepsin in complex with fragment 162 -

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Basic information

Entry
Database: PDB / ID: 4y47
TitleEndothiapepsin in complex with fragment 162
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
Chem-479 / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.19 Å
AuthorsKrimmer, S.G. / Krug, M. / Uehlein, M. / 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: Krimmer, S.G. / 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
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)34,3455
Polymers33,8141
Non-polymers5324
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-2 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.285, 72.766, 52.630
Angle α, β, γ (deg.)90.00, 109.38, 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-479 / 4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide


Mass: 288.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N2O2S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.92 %
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: 0.8944 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8944 Å / Relative weight: 1
ReflectionResolution: 1.19→42.72 Å / Num. obs: 102282 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.065 / Net I/σ(I): 14.5
Reflection shellResolution: 1.19→1.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.04 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIXdev_1779refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementResolution: 1.19→36.38 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1536 5113 5 %random selection
Rwork0.1316 ---
obs0.1327 102263 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.19→36.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 36 333 2734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062518
X-RAY DIFFRACTIONf_angle_d1.2223459
X-RAY DIFFRACTIONf_dihedral_angle_d10.754829
X-RAY DIFFRACTIONf_chiral_restr0.071408
X-RAY DIFFRACTIONf_plane_restr0.006458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.188-1.20150.28521400.27792667X-RAY DIFFRACTION82
1.2015-1.21570.27641600.25383044X-RAY DIFFRACTION94
1.2157-1.23050.25141700.22163223X-RAY DIFFRACTION97
1.2305-1.24610.2241700.19923219X-RAY DIFFRACTION100
1.2461-1.26250.22271710.18783263X-RAY DIFFRACTION100
1.2625-1.27980.20691710.17813232X-RAY DIFFRACTION100
1.2798-1.29810.23251730.17263286X-RAY DIFFRACTION100
1.2981-1.31740.19181720.16133267X-RAY DIFFRACTION100
1.3174-1.3380.1881700.15513239X-RAY DIFFRACTION99
1.338-1.360.17311710.15143257X-RAY DIFFRACTION100
1.36-1.38340.17121730.1423278X-RAY DIFFRACTION100
1.3834-1.40860.15161680.14243192X-RAY DIFFRACTION100
1.4086-1.43570.16011710.13623258X-RAY DIFFRACTION100
1.4357-1.4650.15991750.13163310X-RAY DIFFRACTION100
1.465-1.49680.15341710.12713253X-RAY DIFFRACTION100
1.4968-1.53160.14961710.11753244X-RAY DIFFRACTION100
1.5316-1.56990.12331720.1043268X-RAY DIFFRACTION100
1.5699-1.61240.11581720.09853270X-RAY DIFFRACTION100
1.6124-1.65980.15121720.10333267X-RAY DIFFRACTION100
1.6598-1.71340.13821710.10283256X-RAY DIFFRACTION100
1.7134-1.77470.13561730.10343278X-RAY DIFFRACTION100
1.7747-1.84570.14151720.10483264X-RAY DIFFRACTION100
1.8457-1.92970.13081710.10463263X-RAY DIFFRACTION100
1.9297-2.03140.12161730.10543289X-RAY DIFFRACTION100
2.0314-2.15870.11921720.10263267X-RAY DIFFRACTION100
2.1587-2.32530.12221730.11463283X-RAY DIFFRACTION100
2.3253-2.55930.14141730.1223280X-RAY DIFFRACTION100
2.5593-2.92950.14011720.12743280X-RAY DIFFRACTION100
2.9295-3.69030.16141740.13713301X-RAY DIFFRACTION100
3.6903-36.40010.16121760.15153352X-RAY DIFFRACTION100

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