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- PDB-4y57: Endothiapepsin in complex with fragment 63 -

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Basic information

Entry
Database: PDB / ID: 4y57
TitleEndothiapepsin in complex with fragment 63
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 / Chem-F63 / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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
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)34,3236
Polymers33,8141
Non-polymers5105
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint2 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.573, 73.319, 53.051
Angle α, β, γ (deg.)90.00, 109.93, 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, 329 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-F63 / N-methyl-1-[5-(pyridin-3-yloxy)furan-2-yl]methanamine


Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 1.93 Å3/Da / Density % sol: 36.11 %
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

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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 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.49→42.84 Å / Num. obs: 53579 / % possible obs: 99.8 % / Redundancy: 4.15 % / Rsym value: 0.075 / Net I/σ(I): 13.47
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 4.15 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.92 / % possible all: 99.6

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Processing

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

3pcw


Resolution: 1.49→39.912 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1525 2679 5 %
Rwork0.1174 --
obs0.1191 53574 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→39.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 35 324 2728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082544
X-RAY DIFFRACTIONf_angle_d1.1573497
X-RAY DIFFRACTIONf_dihedral_angle_d10.705836
X-RAY DIFFRACTIONf_chiral_restr0.07411
X-RAY DIFFRACTIONf_plane_restr0.006465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4895-1.51660.25561400.18382661X-RAY DIFFRACTION99
1.5166-1.54580.19371390.14982649X-RAY DIFFRACTION100
1.5458-1.57730.19331410.13442685X-RAY DIFFRACTION100
1.5773-1.61160.16881410.12092666X-RAY DIFFRACTION100
1.6116-1.64910.16771400.11682662X-RAY DIFFRACTION100
1.6491-1.69040.191410.10662679X-RAY DIFFRACTION100
1.6904-1.73610.15811390.10582637X-RAY DIFFRACTION100
1.7361-1.78710.14531420.10242704X-RAY DIFFRACTION100
1.7871-1.84480.16881400.10152661X-RAY DIFFRACTION100
1.8448-1.91080.15421400.09912660X-RAY DIFFRACTION100
1.9108-1.98730.13771420.09432690X-RAY DIFFRACTION100
1.9873-2.07770.12731400.09262666X-RAY DIFFRACTION100
2.0777-2.18720.12861420.09132697X-RAY DIFFRACTION100
2.1872-2.32430.14241410.10012671X-RAY DIFFRACTION100
2.3243-2.50370.12651410.10742681X-RAY DIFFRACTION100
2.5037-2.75560.14571400.11622676X-RAY DIFFRACTION100
2.7556-3.15420.13641420.12352693X-RAY DIFFRACTION100
3.1542-3.97340.15761420.1322703X-RAY DIFFRACTION100
3.9734-39.9260.15971460.14432754X-RAY DIFFRACTION100

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