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- PDB-4ycy: Endothiapepsin in complex with fragment 218 -

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Basic information

Entry
Database: PDB / ID: 4ycy
TitleEndothiapepsin in complex with fragment 218
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-(4-ethoxy-8-methylquinazolin-2-yl)guanidine / DI(HYDROXYETHYL)ETHER / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 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 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,3495
Polymers33,8141
Non-polymers5364
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint1 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.564, 72.903, 52.710
Angle α, β, γ (deg.)90.00, 108.75, 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-4AO / 2-(4-ethoxy-8-methylquinazolin-2-yl)guanidine


Mass: 245.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O
#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-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.92 Å3/Da / Density % sol: 35.79 %
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: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.699→19.23 Å / Num. obs: 35184 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.058 / Net I/σ(I): 19.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIXdev_1779refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.699→19.225 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 1791 5 %Random selection
Rwork0.1657 ---
obs0.1673 35813 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→19.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 35 164 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062438
X-RAY DIFFRACTIONf_angle_d1.0343348
X-RAY DIFFRACTIONf_dihedral_angle_d10.718797
X-RAY DIFFRACTIONf_chiral_restr0.042400
X-RAY DIFFRACTIONf_plane_restr0.004443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6994-1.74530.26021340.20572550X-RAY DIFFRACTION97
1.7453-1.79670.24941350.19082568X-RAY DIFFRACTION100
1.7967-1.85460.22091380.17922609X-RAY DIFFRACTION100
1.8546-1.92080.19141360.16652601X-RAY DIFFRACTION100
1.9208-1.99770.1841380.15192617X-RAY DIFFRACTION100
1.9977-2.08850.18421380.14592623X-RAY DIFFRACTION100
2.0885-2.19840.17521380.14322617X-RAY DIFFRACTION100
2.1984-2.3360.18981370.1522611X-RAY DIFFRACTION100
2.336-2.5160.22351400.1622652X-RAY DIFFRACTION100
2.516-2.76850.19331370.16882610X-RAY DIFFRACTION100
2.7685-3.16760.1921390.16392638X-RAY DIFFRACTION100
3.1676-3.98490.19191390.16912634X-RAY DIFFRACTION100
3.9849-19.2260.19751420.17252692X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.26770.26150.13690.7270.040.6823-0.0116-0.14820.10770.2319-0.01820.10190.0497-0.1848-0.00090.172-0.00930.01530.165-0.00840.1330.7741-9.258714.8739
20.12050.0784-0.05920.0668-0.01210.0638-0.1296-0.13330.09910.12630.13380.0155-0.1124-0.4011-0.00220.43720.0552-0.03670.3022-0.01150.15985.8215-5.120628.975
30.0553-0.0573-0.03990.5627-0.09250.8434-0.0641-0.20730.10890.24530.01380.0037-0.0092-0.089-0.00130.2111-0.003-0.03430.1896-0.03810.17567.0311-3.509419.2809
40.2869-0.0325-0.33540.3243-0.20310.5748-0.0144-0.01260.0224-0.033-0.0337-0.16830.00460.0328-0.02450.09320.0045-0.01190.11970.01560.189814.692-4.9211-0.4098
50.092-0.0995-0.0530.20350.00270.060.08520.0785-0.03470.08740.0842-0.1011-0.03740.01450.00010.145-0.00330.00250.1364-0.00020.191410.044210.9458-0.6125
60.1785-0.05620.10320.4941-0.04770.25760.00880.01280.0341-0.0705-0.0055-0.107-0.0076-0.0689-0.00220.11740.00140.01620.09630.0070.0970.882811.0208-7.7119
70.2728-0.4627-0.2250.82280.2550.7454-0.16390.12740.0773-0.01560.09440.00860.0411-0.1389-0.3450.1361-0.04580.04230.1939-0.0680.0911-13.71957.996-8.0788
80.3796-0.48450.02910.6873-0.22720.50540.00730.0665-0.0562-0.0329-0.0437-0.1296-0.02840.0174-0.01230.0965-0.00630.0140.102-0.00620.12032.75863.843-4.5606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:62)
2X-RAY DIFFRACTION2(chain A and resid 63:77)
3X-RAY DIFFRACTION3(chain A and resid 85:151)
4X-RAY DIFFRACTION4(chain A and resid 152:190)
5X-RAY DIFFRACTION5(chain A and resid 191:204)
6X-RAY DIFFRACTION6(chain A and resid 205:242)
7X-RAY DIFFRACTION7(chain A and resid 243:258)
8X-RAY DIFFRACTION8(chain A and resid 259:330)

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