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- PDB-4yck: Endothiapepsin in complex with fragment 211 -

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Basic information

Entry
Database: PDB / ID: 4yck
TitleEndothiapepsin in complex with fragment 211
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
ethyl 4-(aminomethyl)benzoate / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsStieler, 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: Stieler, M. / 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 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 30, 2019Group: Advisory / Atomic model / Data collection
Category: atom_site / atom_site_anisotrop / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol
Revision 2.1Jan 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 2.2Oct 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)34,4998
Polymers33,8141
Non-polymers6857
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-0 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.311, 72.976, 52.806
Angle α, β, γ (deg.)90.00, 109.67, 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, 309 molecules

#2: Chemical ChemComp-78B / ethyl 4-(aminomethyl)benzoate


Mass: 179.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: 35.25 %
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: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.07→42.67 Å / Num. obs: 137772 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.048 / Net I/σ(I): 14.2
Reflection shellResolution: 1.07→1.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.2 / % possible all: 94

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Processing

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

3pcw


Resolution: 1.07→36.488 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 11.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1358 6888 5 %Random selection
Rwork0.1185 ---
obs0.1193 137767 96.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.07→36.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 44 302 2719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062608
X-RAY DIFFRACTIONf_angle_d1.2213585
X-RAY DIFFRACTIONf_dihedral_angle_d10.414873
X-RAY DIFFRACTIONf_chiral_restr0.07416
X-RAY DIFFRACTIONf_plane_restr0.006480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0696-1.08170.24332160.22734112X-RAY DIFFRACTION92
1.0817-1.09450.22122240.20984241X-RAY DIFFRACTION94
1.0945-1.10780.20682240.19054266X-RAY DIFFRACTION94
1.1078-1.12180.1672230.1714226X-RAY DIFFRACTION95
1.1218-1.13660.18462250.16464282X-RAY DIFFRACTION95
1.1366-1.15220.15562240.1514249X-RAY DIFFRACTION95
1.1522-1.16860.16592260.13944301X-RAY DIFFRACTION95
1.1686-1.18610.1642260.13584296X-RAY DIFFRACTION95
1.1861-1.20460.13962250.1264270X-RAY DIFFRACTION96
1.2046-1.22440.13442270.12344318X-RAY DIFFRACTION96
1.2244-1.24550.16152260.12514292X-RAY DIFFRACTION96
1.2455-1.26810.1332270.12184323X-RAY DIFFRACTION96
1.2681-1.29250.15972290.1254340X-RAY DIFFRACTION96
1.2925-1.31890.15012290.11654344X-RAY DIFFRACTION97
1.3189-1.34760.13852270.10744328X-RAY DIFFRACTION97
1.3476-1.37890.14352310.09874378X-RAY DIFFRACTION97
1.3789-1.41340.12492280.09394337X-RAY DIFFRACTION97
1.4134-1.45160.11752310.09224386X-RAY DIFFRACTION97
1.4516-1.49440.11062310.08974387X-RAY DIFFRACTION98
1.4944-1.54260.11352310.08884393X-RAY DIFFRACTION98
1.5426-1.59770.11442320.08714415X-RAY DIFFRACTION98
1.5977-1.66170.10772340.08724437X-RAY DIFFRACTION98
1.6617-1.73730.10772340.08844458X-RAY DIFFRACTION98
1.7373-1.82890.11552340.09334437X-RAY DIFFRACTION99
1.8289-1.94350.11992350.09424470X-RAY DIFFRACTION99
1.9435-2.09350.10152360.09394477X-RAY DIFFRACTION99
2.0935-2.30420.12222360.09894492X-RAY DIFFRACTION99
2.3042-2.63750.11312370.11514504X-RAY DIFFRACTION100
2.6375-3.32270.13512390.12344538X-RAY DIFFRACTION100
3.3227-36.50920.16572410.15184582X-RAY DIFFRACTION100

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