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- PDB-4y5c: Endothiapepsin in complex with fragment 267 -

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Basic information

Entry
Database: PDB / ID: 4y5c
TitleEndothiapepsin in complex with fragment 267
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
2,5-dimethyl-N-(pyridin-4-yl)furan-3-carboxamide / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsWang, X. / 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: Wang, X. / 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 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)34,3656
Polymers33,8141
Non-polymers5525
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-2 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.277, 73.054, 52.798
Angle α, β, γ (deg.)90.00, 109.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#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.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-47V / 2,5-dimethyl-N-(pyridin-4-yl)furan-3-carboxamide


Mass: 216.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
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: 35.38 %
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: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.19→42.717 Å / Num. obs: 104430 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.54 % / Rsym value: 0.037 / Net I/σ(I): 17.98
Reflection shellResolution: 1.19→1.26 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.24 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCW

3pcw


Resolution: 1.19→39.545 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1405 5175 5 %Random selection
Rwork0.1154 ---
obs0.1166 103484 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.19→39.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 38 277 2689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062550
X-RAY DIFFRACTIONf_angle_d1.2013505
X-RAY DIFFRACTIONf_dihedral_angle_d10.449845
X-RAY DIFFRACTIONf_chiral_restr0.07410
X-RAY DIFFRACTIONf_plane_restr0.006466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1874-1.20090.2341490.22272822X-RAY DIFFRACTION86
1.2009-1.2150.2491740.19223308X-RAY DIFFRACTION100
1.215-1.22980.21191710.18253255X-RAY DIFFRACTION100
1.2298-1.24540.20791740.16823290X-RAY DIFFRACTION100
1.2454-1.26180.20661720.15913278X-RAY DIFFRACTION99
1.2618-1.2790.19521720.15563259X-RAY DIFFRACTION100
1.279-1.29730.15641730.14853290X-RAY DIFFRACTION100
1.2973-1.31670.17161720.13453277X-RAY DIFFRACTION100
1.3167-1.33730.1731730.13323293X-RAY DIFFRACTION100
1.3373-1.35920.15611730.12193275X-RAY DIFFRACTION100
1.3592-1.38260.1611730.12053285X-RAY DIFFRACTION99
1.3826-1.40780.12211720.10963282X-RAY DIFFRACTION99
1.4078-1.43480.15231730.10333273X-RAY DIFFRACTION100
1.4348-1.46410.14061740.09853306X-RAY DIFFRACTION100
1.4641-1.4960.1361720.09443274X-RAY DIFFRACTION100
1.496-1.53080.11351730.08423292X-RAY DIFFRACTION100
1.5308-1.56910.11031750.07933315X-RAY DIFFRACTION100
1.5691-1.61150.11211730.08123287X-RAY DIFFRACTION100
1.6115-1.65890.12841740.08143300X-RAY DIFFRACTION100
1.6589-1.71240.11251730.08223292X-RAY DIFFRACTION100
1.7124-1.77360.12191730.0853298X-RAY DIFFRACTION100
1.7736-1.84470.10751740.08663295X-RAY DIFFRACTION100
1.8447-1.92860.11551720.08973263X-RAY DIFFRACTION99
1.9286-2.03030.10511750.09033340X-RAY DIFFRACTION100
2.0303-2.15750.10781740.08973302X-RAY DIFFRACTION100
2.1575-2.3240.1181710.0993251X-RAY DIFFRACTION99
2.324-2.55790.12251740.11093298X-RAY DIFFRACTION100
2.5579-2.92790.13221750.12073326X-RAY DIFFRACTION100
2.9279-3.68840.14631740.13043310X-RAY DIFFRACTION99
3.6884-39.56670.18391780.15173373X-RAY DIFFRACTION99

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