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- PDB-4y3r: Endothiapepsin in complex with fragment 306 -

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Basic information

Entry
Database: PDB / ID: 4y3r
TitleEndothiapepsin in complex with fragment 306
ComponentsEndothiapepsin
KeywordsHYDROLASE / fragment screening / aspartic protease / 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 / 2-chlorobenzyl carbamimidothioate / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsWang, X. / 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: 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 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name
Revision 1.2Oct 9, 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)34,3366
Polymers33,8141
Non-polymers5225
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint1 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.218, 73.159, 52.735
Angle α, β, γ (deg.)90.00, 109.61, 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, 295 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-F06 / 2-chlorobenzyl carbamimidothioate


Mass: 200.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9ClN2S
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 35.21 %
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 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.13→42.6 Å / Num. obs: 120427 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.041 / Net I/σ(I): 16.7
Reflection shellResolution: 1.13→1.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→28.023 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1413 6022 5 %random selection
Rwork0.1237 ---
obs0.1246 120424 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.13→28.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 32 290 2695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062566
X-RAY DIFFRACTIONf_angle_d1.2353528
X-RAY DIFFRACTIONf_dihedral_angle_d10.905845
X-RAY DIFFRACTIONf_chiral_restr0.07412
X-RAY DIFFRACTIONf_plane_restr0.006466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1293-1.14220.21141960.21453710X-RAY DIFFRACTION98
1.1422-1.15560.21311990.19253792X-RAY DIFFRACTION100
1.1556-1.16970.18092000.18233802X-RAY DIFFRACTION100
1.1697-1.18450.21582000.17513792X-RAY DIFFRACTION100
1.1845-1.20010.17532000.16583813X-RAY DIFFRACTION100
1.2001-1.21650.18152010.16043814X-RAY DIFFRACTION100
1.2165-1.23390.18572010.15643808X-RAY DIFFRACTION100
1.2339-1.25230.15212010.14463823X-RAY DIFFRACTION100
1.2523-1.27190.15131980.14373772X-RAY DIFFRACTION100
1.2719-1.29270.16852040.14483868X-RAY DIFFRACTION100
1.2927-1.3150.17281980.13553758X-RAY DIFFRACTION100
1.315-1.33890.16392000.13353810X-RAY DIFFRACTION100
1.3389-1.36470.17122030.12573859X-RAY DIFFRACTION100
1.3647-1.39250.13221990.11443774X-RAY DIFFRACTION100
1.3925-1.42280.11782020.10533834X-RAY DIFFRACTION100
1.4228-1.45590.12412020.09663837X-RAY DIFFRACTION100
1.4559-1.49230.12131990.09653790X-RAY DIFFRACTION100
1.4923-1.53270.11772010.09613806X-RAY DIFFRACTION100
1.5327-1.57780.11482000.09533806X-RAY DIFFRACTION100
1.5778-1.62870.10772020.08883839X-RAY DIFFRACTION100
1.6287-1.68690.11052010.09113821X-RAY DIFFRACTION100
1.6869-1.75440.11732010.09663811X-RAY DIFFRACTION100
1.7544-1.83430.11882010.10023836X-RAY DIFFRACTION100
1.8343-1.93090.11842010.10193806X-RAY DIFFRACTION100
1.9309-2.05190.12762020.10173851X-RAY DIFFRACTION100
2.0519-2.21030.11312000.10213799X-RAY DIFFRACTION99
2.2103-2.43260.12752010.11413813X-RAY DIFFRACTION100
2.4326-2.78430.13882020.12453835X-RAY DIFFRACTION99
2.7843-3.50680.15162020.13563833X-RAY DIFFRACTION99
3.5068-28.03120.16442050.15063890X-RAY DIFFRACTION99

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