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- PDB-4y3l: Endothiapepsin in complex with fragment 205 -

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Basic information

Entry
Database: PDB / ID: 4y3l
TitleEndothiapepsin in complex with fragment 205
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
ACETATE ION / THIOPHENE-3-CARBOXIMIDAMIDE / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsEhrmann, F.R. / Huschmann, F.U. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
BMBF05K13RM1 Germany
Citation
Journal: To Be Published
Title: Crystallographic Fragment Sreening of an Entire Library
Authors: Ehrmann, F.R. / 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 1.1Jan 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
Revision 1.2Nov 13, 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)34,99914
Polymers33,8141
Non-polymers1,18513
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint2 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.200, 72.860, 52.576
Angle α, β, γ (deg.)90.00, 109.47, 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, 311 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-TP5 / THIOPHENE-3-CARBOXIMIDAMIDE


Mass: 126.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N2S
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.78 %
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 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8944 Å / Relative weight: 1
ReflectionResolution: 1.16→42.615 Å / Num. obs: 108943 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.05 / Net I/σ(I): 17.43
Reflection shellResolution: 1.16→1.23 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.23 / % possible all: 87.9

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Processing

Software
NameVersionClassification
PHENIXdev_1779refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCW

3pcw


Resolution: 1.16→29.355 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.132 5447 5 %random selection
Rwork0.1163 ---
obs0.1171 108935 98.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.16→29.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 76 298 2748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062605
X-RAY DIFFRACTIONf_angle_d1.2293573
X-RAY DIFFRACTIONf_dihedral_angle_d10.868885
X-RAY DIFFRACTIONf_chiral_restr0.071418
X-RAY DIFFRACTIONf_plane_restr0.006471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1591-1.17220.2221410.21712665X-RAY DIFFRACTION77
1.1722-1.1860.20921550.19112950X-RAY DIFFRACTION84
1.186-1.20050.19111650.17973142X-RAY DIFFRACTION90
1.2005-1.21570.19241750.17113316X-RAY DIFFRACTION95
1.2157-1.23170.1821840.1573495X-RAY DIFFRACTION99
1.2317-1.24860.16891840.14093491X-RAY DIFFRACTION100
1.2486-1.26640.15641830.13493476X-RAY DIFFRACTION100
1.2664-1.28530.1581850.12673526X-RAY DIFFRACTION100
1.2853-1.30540.15771840.12663488X-RAY DIFFRACTION100
1.3054-1.32680.14121850.11643528X-RAY DIFFRACTION100
1.3268-1.34970.12321850.11423515X-RAY DIFFRACTION100
1.3497-1.37420.13921840.11053486X-RAY DIFFRACTION100
1.3742-1.40060.11391850.10473507X-RAY DIFFRACTION100
1.4006-1.42920.12911840.10633511X-RAY DIFFRACTION100
1.4292-1.46030.13891860.10273526X-RAY DIFFRACTION100
1.4603-1.49430.12561840.09783499X-RAY DIFFRACTION100
1.4943-1.53160.11341830.09253482X-RAY DIFFRACTION100
1.5316-1.5730.1071850.0883518X-RAY DIFFRACTION100
1.573-1.61930.10791870.08533537X-RAY DIFFRACTION100
1.6193-1.67160.10311840.08443505X-RAY DIFFRACTION100
1.6716-1.73130.10941860.08823530X-RAY DIFFRACTION100
1.7313-1.80060.10911840.09123492X-RAY DIFFRACTION100
1.8006-1.88260.1181860.09353542X-RAY DIFFRACTION100
1.8826-1.98180.11071830.09473470X-RAY DIFFRACTION100
1.9818-2.10590.10681870.09243565X-RAY DIFFRACTION100
2.1059-2.26850.12141850.09523517X-RAY DIFFRACTION100
2.2685-2.49670.11781870.11043538X-RAY DIFFRACTION100
2.4967-2.85770.11381850.11683527X-RAY DIFFRACTION100
2.8577-3.59930.14781870.12833545X-RAY DIFFRACTION100
3.5993-29.36450.15311890.15513599X-RAY DIFFRACTION100

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