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- PDB-5dq5: Endothiapepsin in complex with fragment 209 -

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Basic information

Entry
Database: PDB / ID: 5dq5
TitleEndothiapepsin in complex with fragment 209
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
3-[2-(4-methyl-1,2-oxazol-3-yl)ethyl]pyridine / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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
DepositionSep 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 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)34,3376
Polymers33,8141
Non-polymers5245
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-2 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.281, 72.986, 52.598
Angle α, β, γ (deg.)90.00, 109.47, 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 / Mutation: UNP residues 90-419 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-5HS / 3-[2-(4-methyl-1,2-oxazol-3-yl)ethyl]pyridine


Mass: 188.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
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: 14.3 / Wavelength: 0.918409 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.47→41.018 Å / Num. obs: 54315 / % possible obs: 98.9 % / Redundancy: 3.69 % / Rsym value: 0.06 / Net I/σ(I): 16.42
Reflection shellResolution: 1.47→1.56 Å / Redundancy: 3.44 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.55 / % possible all: 97.5

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Processing

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

3pcw


Resolution: 1.47→36.493 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1575 2715 5 %
Rwork0.1301 --
obs0.1315 54311 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→36.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 29 279 2677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082534
X-RAY DIFFRACTIONf_angle_d1.2323481
X-RAY DIFFRACTIONf_dihedral_angle_d11.036826
X-RAY DIFFRACTIONf_chiral_restr0.069410
X-RAY DIFFRACTIONf_plane_restr0.005456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.49670.22511380.18512630X-RAY DIFFRACTION97
1.4967-1.52550.21811410.16642666X-RAY DIFFRACTION98
1.5255-1.55660.19771400.15372660X-RAY DIFFRACTION98
1.5566-1.59050.20741420.1462713X-RAY DIFFRACTION98
1.5905-1.62750.17641420.13712692X-RAY DIFFRACTION99
1.6275-1.66820.17051430.12692715X-RAY DIFFRACTION99
1.6682-1.71330.17221410.11752685X-RAY DIFFRACTION99
1.7133-1.76370.17811430.11772716X-RAY DIFFRACTION99
1.7637-1.82060.16961440.11482725X-RAY DIFFRACTION99
1.8206-1.88570.14391440.11042733X-RAY DIFFRACTION99
1.8857-1.96120.14931430.10712723X-RAY DIFFRACTION99
1.9612-2.05040.15151420.1062702X-RAY DIFFRACTION99
2.0504-2.15850.1441430.10432719X-RAY DIFFRACTION99
2.1585-2.29370.14281440.10612731X-RAY DIFFRACTION100
2.2937-2.47080.13061440.11752731X-RAY DIFFRACTION100
2.4708-2.71930.14551440.12412751X-RAY DIFFRACTION100
2.7193-3.11270.13261440.13032738X-RAY DIFFRACTION100
3.1127-3.92090.16921450.14172754X-RAY DIFFRACTION100
3.9209-36.50420.1551480.1622812X-RAY DIFFRACTION100

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