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- PDB-5dr0: Endothiapepsin in complex with fragment 203 -

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Basic information

Entry
Database: PDB / ID: 5dr0
TitleEndothiapepsin in complex with fragment 203
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
Chem-5GC / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSchiebel, J. / 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: Schiebel, J. / 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 15, 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 6, 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)34,79912
Polymers33,8141
Non-polymers98511
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint5 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.249, 73.035, 52.712
Angle α, β, γ (deg.)90.00, 109.16, 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 / Fragment: UNP residues 90-419 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin

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Non-polymers , 6 types, 300 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-5GC / 5-(methylsulfanyl)-4-(propan-2-ylsulfonyl)-1H-pyrazol-3-amine


Mass: 235.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
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: 0.8944 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8944 Å / Relative weight: 1
ReflectionResolution: 1.4→42.7 Å / Num. obs: 63639 / % possible obs: 99.5 % / Redundancy: 3.9 % / Rsym value: 0.062 / Net I/σ(I): 15.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.1 / Num. unique all: 10178 / % possible all: 98.6

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Processing

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

3pcw


Resolution: 1.4→29.447 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1432 3182 5 %
Rwork0.1171 --
obs0.1184 63636 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→29.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 60 289 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072582
X-RAY DIFFRACTIONf_angle_d1.1823546
X-RAY DIFFRACTIONf_dihedral_angle_d10.906840
X-RAY DIFFRACTIONf_chiral_restr0.067416
X-RAY DIFFRACTIONf_plane_restr0.006466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3986-1.41950.18991320.15762508X-RAY DIFFRACTION95
1.4195-1.44170.1911380.15062625X-RAY DIFFRACTION100
1.4417-1.46530.19531400.14292656X-RAY DIFFRACTION100
1.4653-1.49060.1851360.14132601X-RAY DIFFRACTION100
1.4906-1.51770.16691380.13272620X-RAY DIFFRACTION100
1.5177-1.54690.17061400.12322644X-RAY DIFFRACTION100
1.5469-1.57850.16351370.11732613X-RAY DIFFRACTION100
1.5785-1.61280.15561390.11022634X-RAY DIFFRACTION100
1.6128-1.65030.15251380.10382624X-RAY DIFFRACTION100
1.6503-1.69160.13121390.09972640X-RAY DIFFRACTION100
1.6916-1.73730.14581380.09662633X-RAY DIFFRACTION100
1.7373-1.78840.13041380.09342606X-RAY DIFFRACTION100
1.7884-1.84610.1321380.09032630X-RAY DIFFRACTION100
1.8461-1.91210.12181390.08982639X-RAY DIFFRACTION100
1.9121-1.98860.11951370.08762604X-RAY DIFFRACTION100
1.9886-2.07910.10761390.08732643X-RAY DIFFRACTION100
2.0791-2.18870.11221390.08762645X-RAY DIFFRACTION99
2.1887-2.32580.12281380.09742620X-RAY DIFFRACTION100
2.3258-2.50530.12951390.10732640X-RAY DIFFRACTION99
2.5053-2.75720.1421380.11542617X-RAY DIFFRACTION100
2.7572-3.15580.13431390.1222644X-RAY DIFFRACTION100
3.1558-3.97440.16961400.13382662X-RAY DIFFRACTION100
3.9744-29.45330.15161430.16022706X-RAY DIFFRACTION100

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