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- PDB-4y56: Endothiapepsin in complex with fragment 58 -

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Basic information

Entry
Database: PDB / ID: 4y56
TitleEndothiapepsin in complex with fragment 58
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
1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsRadeva, N. / 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: Radeva, N. / 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)34,3287
Polymers33,8141
Non-polymers5146
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint9 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.174, 72.773, 52.528
Angle α, β, γ (deg.)90.00, 109.67, 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, 361 molecules

#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-47J / 1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine


Mass: 125.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 1.88 Å3/Da / Density % sol: 34.53 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.8912 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8912 Å / Relative weight: 1
ReflectionResolution: 1.63→42.54 Å / Num. obs: 39838 / % possible obs: 99.4 % / Redundancy: 4.15 % / Rsym value: 0.057 / Net I/σ(I): 20.08
Reflection shellResolution: 1.63→1.73 Å / Redundancy: 4.01 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 4.35 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1492refinement
Cootmodel building
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCW

3pcw


Resolution: 1.63→25.419 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.171 1989 5 %
Rwork0.1425 --
obs0.144 39772 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→25.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 31 355 2760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012559
X-RAY DIFFRACTIONf_angle_d1.273516
X-RAY DIFFRACTIONf_dihedral_angle_d10.507838
X-RAY DIFFRACTIONf_chiral_restr0.06413
X-RAY DIFFRACTIONf_plane_restr0.006460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6297-1.67050.21981410.18382672X-RAY DIFFRACTION99
1.6705-1.71560.21091410.16362695X-RAY DIFFRACTION100
1.7156-1.76610.18391410.15322691X-RAY DIFFRACTION100
1.7661-1.82310.16421440.14422701X-RAY DIFFRACTION100
1.8231-1.88820.16481420.13562696X-RAY DIFFRACTION100
1.8882-1.96380.17191420.12762710X-RAY DIFFRACTION100
1.9638-2.05310.16431420.12652670X-RAY DIFFRACTION100
2.0531-2.16130.14991430.12652723X-RAY DIFFRACTION100
2.1613-2.29660.16451410.13832683X-RAY DIFFRACTION100
2.2966-2.47380.17791430.14262707X-RAY DIFFRACTION100
2.4738-2.72250.19091430.14692710X-RAY DIFFRACTION100
2.7225-3.11590.17941430.14592719X-RAY DIFFRACTION100
3.1159-3.92330.15251420.13872710X-RAY DIFFRACTION99
3.9233-25.42250.16661410.1492696X-RAY DIFFRACTION97

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