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- PDB-5hco: Endothiapepsin in complex with hydrazide -

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Basic information

Entry
Database: PDB / ID: 5hco
TitleEndothiapepsin in complex with hydrazide
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
4-(dimethylamino)benzohydrazide / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 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
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: 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)34,4767
Polymers33,8141
Non-polymers6626
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint5 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.247, 72.936, 52.730
Angle α, β, γ (deg.)90.00, 109.15, 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 , 6 types, 295 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-601 / 4-(dimethylamino)benzohydrazide


Mass: 179.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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: 1.9 Å3/Da / Density % sol: 35.23 %
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: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.17→42.74 Å / Num. obs: 108391 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rsym value: 0.036 / Net I/σ(I): 16.78
Reflection shellResolution: 1.17→1.24 Å / Redundancy: 3.52 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.63 / % possible all: 96.9

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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: 1.17→42.74 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1432 5420 5 %
Rwork0.1249 --
obs0.1258 108387 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.17→42.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 44 289 2703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062583
X-RAY DIFFRACTIONf_angle_d1.2163550
X-RAY DIFFRACTIONf_dihedral_angle_d10.05853
X-RAY DIFFRACTIONf_chiral_restr0.068416
X-RAY DIFFRACTIONf_plane_restr0.006468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1689-1.18220.22111530.21332904X-RAY DIFFRACTION86
1.1822-1.19610.2181830.18513481X-RAY DIFFRACTION100
1.1961-1.21070.19271810.17653427X-RAY DIFFRACTION100
1.2107-1.2260.18581800.17633438X-RAY DIFFRACTION100
1.226-1.24220.21591810.16483431X-RAY DIFFRACTION100
1.2422-1.25920.16891810.15893445X-RAY DIFFRACTION100
1.2592-1.27720.17111810.15863428X-RAY DIFFRACTION100
1.2772-1.29620.20271800.15183427X-RAY DIFFRACTION100
1.2962-1.31650.16921820.1443447X-RAY DIFFRACTION100
1.3165-1.33810.17321810.1283455X-RAY DIFFRACTION100
1.3381-1.36120.14711820.12393457X-RAY DIFFRACTION100
1.3612-1.38590.1461820.11623443X-RAY DIFFRACTION100
1.3859-1.41260.14831800.1123427X-RAY DIFFRACTION100
1.4126-1.44140.14181810.10593430X-RAY DIFFRACTION100
1.4414-1.47270.10941820.10163470X-RAY DIFFRACTION100
1.4727-1.5070.11831810.09893444X-RAY DIFFRACTION100
1.507-1.54470.1411810.09873434X-RAY DIFFRACTION100
1.5447-1.58650.1391810.09573436X-RAY DIFFRACTION100
1.5865-1.63310.12371820.09493452X-RAY DIFFRACTION100
1.6331-1.68590.12211810.09643452X-RAY DIFFRACTION100
1.6859-1.74610.13831820.0973445X-RAY DIFFRACTION100
1.7461-1.8160.12961820.09713468X-RAY DIFFRACTION100
1.816-1.89870.11391810.10023432X-RAY DIFFRACTION100
1.8987-1.99880.11291810.09833436X-RAY DIFFRACTION100
1.9988-2.1240.11071830.09773477X-RAY DIFFRACTION100
2.124-2.2880.13271820.10293461X-RAY DIFFRACTION100
2.288-2.51820.13941830.11853479X-RAY DIFFRACTION100
2.5182-2.88250.13711810.12623435X-RAY DIFFRACTION99
2.8825-3.63140.13631820.13683472X-RAY DIFFRACTION100
3.6314-42.77250.16881870.16183534X-RAY DIFFRACTION100

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