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- PDB-4y50: Endothiapepsin in complex with fragment 81 -

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Basic information

Entry
Database: PDB / ID: 4y50
TitleEndothiapepsin in complex with fragment 81
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
3-(dimethylamino)benzohydrazide / ACETATE ION / TRIETHYLENE GLYCOL / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsSchiebel, J. / 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: Schiebel, J. / 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 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 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 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)34,85312
Polymers33,8141
Non-polymers1,03911
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint14 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.286, 73.166, 52.694
Angle α, β, γ (deg.)90.00, 109.39, 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 , 7 types, 279 molecules

#2: Chemical ChemComp-47S / 3-(dimethylamino)benzohydrazide


Mass: 179.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 1.9 Å3/Da / Density % sol: 35.36 %
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: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.32→42.72 Å / Num. obs: 75485 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.095 / Net I/σ(I): 9.2
Reflection shellResolution: 1.32→1.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.6 / % possible all: 98.2

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Processing

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

3pcw


Resolution: 1.32→29.464 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1453 3773 5 %random selection
Rwork0.1209 ---
obs0.1221 75481 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→29.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 65 268 2699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072538
X-RAY DIFFRACTIONf_angle_d1.2373476
X-RAY DIFFRACTIONf_dihedral_angle_d10.948837
X-RAY DIFFRACTIONf_chiral_restr0.071410
X-RAY DIFFRACTIONf_plane_restr0.006449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3198-1.33650.20991370.17432596X-RAY DIFFRACTION98
1.3365-1.35410.20261380.1652631X-RAY DIFFRACTION98
1.3541-1.37260.22191380.15752623X-RAY DIFFRACTION99
1.3726-1.39230.19211380.14262606X-RAY DIFFRACTION99
1.3923-1.4130.15791390.13412639X-RAY DIFFRACTION98
1.413-1.43510.17381370.12222615X-RAY DIFFRACTION99
1.4351-1.45860.17271410.11462683X-RAY DIFFRACTION99
1.4586-1.48380.15031360.11422575X-RAY DIFFRACTION99
1.4838-1.51080.15541410.11092687X-RAY DIFFRACTION99
1.5108-1.53980.14311390.10562626X-RAY DIFFRACTION99
1.5398-1.57130.13091390.10182656X-RAY DIFFRACTION99
1.5713-1.60540.15211390.09672643X-RAY DIFFRACTION99
1.6054-1.64280.13191400.09582643X-RAY DIFFRACTION99
1.6428-1.68380.13861390.09462648X-RAY DIFFRACTION99
1.6838-1.72940.14041400.0952671X-RAY DIFFRACTION100
1.7294-1.78020.12321400.09492654X-RAY DIFFRACTION100
1.7802-1.83770.12711410.09472674X-RAY DIFFRACTION100
1.8377-1.90340.12641390.09642650X-RAY DIFFRACTION100
1.9034-1.97960.10441410.09382674X-RAY DIFFRACTION100
1.9796-2.06960.11111400.09492665X-RAY DIFFRACTION100
2.0696-2.17870.12341420.09532684X-RAY DIFFRACTION100
2.1787-2.31520.12491400.10672672X-RAY DIFFRACTION100
2.3152-2.49380.1271420.11572701X-RAY DIFFRACTION100
2.4938-2.74460.15541410.12632664X-RAY DIFFRACTION100
2.7446-3.14140.15061410.13442689X-RAY DIFFRACTION100
3.1414-3.95630.17541420.14752701X-RAY DIFFRACTION100
3.9563-29.47090.15031430.15672738X-RAY DIFFRACTION100

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