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- PDB-4y3s: Endothiapepsin in complex with fragment 266 -

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Basic information

Entry
Database: PDB / ID: 4y3s
TitleEndothiapepsin in complex with fragment 266
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
6-(dimethylamino)pyridine-3-carboxylic acid / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 Å
AuthorsKrimmer, S.G. / 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: Krimmer, S.G. / 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 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 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)34,1314
Polymers33,8141
Non-polymers3173
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-1 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.251, 73.046, 52.778
Angle α, β, γ (deg.)90.00, 109.50, 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.: 1 / 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-46L / 6-(dimethylamino)pyridine-3-carboxylic acid


Mass: 166.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 35.26 %
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: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.1→19.78 Å / Num. obs: 127054 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.032 / Net I/σ(I): 20.5
Reflection shellResolution: 1.1→1.17 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.7 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIXdev_1779refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PCW

3pcw


Resolution: 1.1→19.779 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1405 6353 5 %random selection
Rwork0.1237 ---
obs0.1245 127037 97.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→19.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 22 273 2667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062527
X-RAY DIFFRACTIONf_angle_d1.2293477
X-RAY DIFFRACTIONf_dihedral_angle_d10.386831
X-RAY DIFFRACTIONf_chiral_restr0.069410
X-RAY DIFFRACTIONf_plane_restr0.006458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0999-1.11240.22731920.2323649X-RAY DIFFRACTION89
1.1124-1.12550.24012000.22173791X-RAY DIFFRACTION92
1.1255-1.13920.17682050.18443897X-RAY DIFFRACTION95
1.1392-1.15360.18262070.16553939X-RAY DIFFRACTION95
1.1536-1.16880.19982080.16293935X-RAY DIFFRACTION95
1.1688-1.18480.15422070.1573934X-RAY DIFFRACTION95
1.1848-1.20170.17012080.14393952X-RAY DIFFRACTION96
1.2017-1.21970.15182090.13383980X-RAY DIFFRACTION96
1.2197-1.23870.13212090.12663964X-RAY DIFFRACTION96
1.2387-1.2590.14812100.12543995X-RAY DIFFRACTION96
1.259-1.28070.14452090.11923970X-RAY DIFFRACTION96
1.2807-1.3040.1292110.11724011X-RAY DIFFRACTION97
1.304-1.32910.12512120.11014024X-RAY DIFFRACTION97
1.3291-1.35620.13082130.11074045X-RAY DIFFRACTION98
1.3562-1.38570.12312140.10534062X-RAY DIFFRACTION98
1.3857-1.41790.12542110.10344025X-RAY DIFFRACTION98
1.4179-1.45340.13292150.09954073X-RAY DIFFRACTION98
1.4534-1.49260.11932130.09734058X-RAY DIFFRACTION98
1.4926-1.53660.12462150.09394076X-RAY DIFFRACTION99
1.5366-1.58610.11012160.09154105X-RAY DIFFRACTION99
1.5861-1.64280.11662150.09514079X-RAY DIFFRACTION99
1.6428-1.70850.10992150.09774098X-RAY DIFFRACTION99
1.7085-1.78620.12642170.10544108X-RAY DIFFRACTION99
1.7862-1.88030.13222170.10574127X-RAY DIFFRACTION99
1.8803-1.99810.12112150.10474085X-RAY DIFFRACTION99
1.9981-2.15210.10952180.10374147X-RAY DIFFRACTION99
2.1521-2.36840.12322160.11474111X-RAY DIFFRACTION99
2.3684-2.71040.14512170.12624110X-RAY DIFFRACTION99
2.7104-3.41190.15792170.13554133X-RAY DIFFRACTION99
3.4119-19.7820.16532220.15124201X-RAY DIFFRACTION99

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