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- PDB-4y5l: Endothiapepsin in its apo form -

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Basic information

Entry
Database: PDB / ID: 4y5l
TitleEndothiapepsin in its apo form
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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 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 1.2Oct 23, 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)34,68210
Polymers33,8141
Non-polymers8689
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-3 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.230, 72.650, 52.480
Angle α, β, γ (deg.)90.00, 109.15, 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, 343 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 1.88 Å3/Da / Density % sol: 34.65 %
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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 0.99→42.73 Å / Num. obs: 177093 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.038 / Net I/σ(I): 18.9
Reflection shellResolution: 0.99→1.05 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.501 / % possible all: 99.7

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Processing

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

3pcw


Resolution: 0.99→42.727 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 10.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1296 8848 5 %random selection
Rwork0.1169 ---
obs0.1175 177077 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.99→42.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 57 334 2760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082590
X-RAY DIFFRACTIONf_angle_d1.3773555
X-RAY DIFFRACTIONf_dihedral_angle_d10.525871
X-RAY DIFFRACTIONf_chiral_restr0.08420
X-RAY DIFFRACTIONf_plane_restr0.008454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9899-1.00120.22362910.20485540X-RAY DIFFRACTION99
1.0012-1.0130.20932950.1915585X-RAY DIFFRACTION100
1.013-1.02530.19122960.17555628X-RAY DIFFRACTION100
1.0253-1.03830.18592940.16675585X-RAY DIFFRACTION100
1.0383-1.0520.16392960.14635617X-RAY DIFFRACTION100
1.052-1.06640.13692910.12585546X-RAY DIFFRACTION100
1.0664-1.08160.14422960.11565608X-RAY DIFFRACTION100
1.0816-1.09780.11942970.10665641X-RAY DIFFRACTION100
1.0978-1.11490.11182920.09835552X-RAY DIFFRACTION100
1.1149-1.13320.10992960.09345623X-RAY DIFFRACTION100
1.1332-1.15270.10682940.09085594X-RAY DIFFRACTION100
1.1527-1.17370.09082950.08545607X-RAY DIFFRACTION100
1.1737-1.19630.10062940.07925616X-RAY DIFFRACTION100
1.1963-1.22070.0962950.07975604X-RAY DIFFRACTION100
1.2207-1.24730.08752950.08075606X-RAY DIFFRACTION100
1.2473-1.27630.10482960.08115614X-RAY DIFFRACTION100
1.2763-1.30820.09012930.08215574X-RAY DIFFRACTION100
1.3082-1.34360.09882970.08445646X-RAY DIFFRACTION100
1.3436-1.38310.10582960.08875629X-RAY DIFFRACTION100
1.3831-1.42770.11512970.08625638X-RAY DIFFRACTION100
1.4277-1.47880.09882940.08535590X-RAY DIFFRACTION100
1.4788-1.5380.10672970.08815646X-RAY DIFFRACTION100
1.538-1.6080.10642940.09085607X-RAY DIFFRACTION100
1.608-1.69280.10772960.09765641X-RAY DIFFRACTION100
1.6928-1.79880.11152950.10855601X-RAY DIFFRACTION100
1.7988-1.93770.13112960.11385626X-RAY DIFFRACTION100
1.9377-2.13270.1212960.11175629X-RAY DIFFRACTION100
2.1327-2.44130.14742970.12785636X-RAY DIFFRACTION100
2.4413-3.07560.15032960.14365648X-RAY DIFFRACTION99
3.0756-42.76720.1562910.14855552X-RAY DIFFRACTION97

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