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- PDB-4y3p: Endothiapepsin in complex with fragment 17 -

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Basic information

Entry
Database: PDB / ID: 4y3p
TitleEndothiapepsin in complex with fragment 17
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
1-(6-methylpyrimidin-4-yl)azepane / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRadeva, N. / Uehlein, M. / Weiss, M.S. / Heine, A. / Klebe, G.
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 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)34,3815
Polymers33,8141
Non-polymers5674
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-1 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.354, 72.720, 52.494
Angle α, β, γ (deg.)90.00, 108.99, 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-46S / 1-(6-methylpyrimidin-4-yl)azepane


Mass: 191.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 1.89 Å3/Da / Density % sol: 34.97 %
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: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.55→42.89 Å / Num. obs: 46729 / % possible obs: 98.9 % / Redundancy: 4.19 % / Rsym value: 0.063 / Net I/σ(I): 17.08
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 4.14 % / Rmerge(I) obs: 0.508 / % possible all: 94.5

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Processing

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

3pcw


Resolution: 1.55→42.886 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1607 2336 5 %
Rwork0.1175 --
obs0.1196 46727 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→42.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 36 313 2719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082519
X-RAY DIFFRACTIONf_angle_d1.1463456
X-RAY DIFFRACTIONf_dihedral_angle_d11.133827
X-RAY DIFFRACTIONf_chiral_restr0.044406
X-RAY DIFFRACTIONf_plane_restr0.006459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5455-1.57710.20921190.15192249X-RAY DIFFRACTION86
1.5771-1.61140.24651370.14632609X-RAY DIFFRACTION100
1.6114-1.64890.2291380.13772619X-RAY DIFFRACTION100
1.6489-1.69010.21011380.12912629X-RAY DIFFRACTION100
1.6901-1.73580.19481390.11592644X-RAY DIFFRACTION100
1.7358-1.78690.15581370.10572607X-RAY DIFFRACTION100
1.7869-1.84450.14521380.10032615X-RAY DIFFRACTION100
1.8445-1.91050.18841380.09932629X-RAY DIFFRACTION100
1.9105-1.9870.14671380.09252623X-RAY DIFFRACTION100
1.987-2.07740.1281390.08842634X-RAY DIFFRACTION100
2.0774-2.18690.13781390.09042642X-RAY DIFFRACTION100
2.1869-2.32390.13811380.09812610X-RAY DIFFRACTION100
2.3239-2.50330.13821400.10592662X-RAY DIFFRACTION100
2.5033-2.75520.15281380.11292623X-RAY DIFFRACTION100
2.7552-3.15380.15651390.11992652X-RAY DIFFRACTION100
3.1538-3.9730.15381390.12712637X-RAY DIFFRACTION100
3.973-42.90240.17531420.15152707X-RAY DIFFRACTION100

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