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- PDB-4y35: Endothiapepsin in complex with fragment 290 -

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Basic information

Entry
Database: PDB / ID: 4y35
TitleEndothiapepsin in complex with fragment 290
ComponentsEndothiapepsin
KeywordsHYDROLASE / fagment 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
ACETATE ION / 4-chlorobenzyl carbamimidothioate / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.457 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 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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)34,4147
Polymers33,8141
Non-polymers6006
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint1 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.251, 73.107, 52.776
Angle α, β, γ (deg.)90.00, 109.53, 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, 274 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-F90 / 4-chlorobenzyl carbamimidothioate


Mass: 200.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9ClN2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 35.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M ammonium acetate, 0.1M 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: 1.46→41.13 Å / Num. obs: 56120 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.062 / Net I/σ(I): 13.3
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.4 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1492refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.457→39.564 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1587 2807 5 %random selection
Rwork0.1248 ---
obs0.1265 56118 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.457→39.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 36 268 2672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072531
X-RAY DIFFRACTIONf_angle_d1.2113473
X-RAY DIFFRACTIONf_dihedral_angle_d10.2827
X-RAY DIFFRACTIONf_chiral_restr0.07408
X-RAY DIFFRACTIONf_plane_restr0.005454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4574-1.48260.21911280.15662435X-RAY DIFFRACTION93
1.4826-1.50950.19491450.14552725X-RAY DIFFRACTION100
1.5095-1.53860.19741380.1322621X-RAY DIFFRACTION100
1.5386-1.570.15411410.12452684X-RAY DIFFRACTION100
1.57-1.60410.17371400.11432646X-RAY DIFFRACTION100
1.6041-1.64140.1551400.11122665X-RAY DIFFRACTION100
1.6414-1.68250.15921400.11152661X-RAY DIFFRACTION100
1.6825-1.7280.16311420.10722685X-RAY DIFFRACTION100
1.728-1.77880.15771400.10372673X-RAY DIFFRACTION100
1.7788-1.83620.16391410.10292677X-RAY DIFFRACTION100
1.8362-1.90180.15941400.10012657X-RAY DIFFRACTION100
1.9018-1.9780.13321410.09882684X-RAY DIFFRACTION100
1.978-2.0680.13211410.09762661X-RAY DIFFRACTION100
2.068-2.1770.12451410.0982687X-RAY DIFFRACTION100
2.177-2.31340.1291410.11182677X-RAY DIFFRACTION100
2.3134-2.4920.14241410.11692674X-RAY DIFFRACTION99
2.492-2.74270.14741400.12672668X-RAY DIFFRACTION100
2.7427-3.13950.16261420.1322696X-RAY DIFFRACTION100
3.1395-3.95480.1711400.14632693X-RAY DIFFRACTION100
3.9548-39.57880.18311450.15562742X-RAY DIFFRACTION99

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