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- PDB-4lhh: Endothiapepsin in complex with 2mM acylhydrazone inhibitor -

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Basic information

Entry
Database: PDB / ID: 4lhh
TitleEndothiapepsin in complex with 2mM acylhydrazone inhibitor
ComponentsEndothiapepsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Hydrolase / Aspartic protease / HYDROLASE-HYDROLASE INHIBITOR complex
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-1TZ / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsRadeva, N. / Heine, A. / Klebe, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Structure-based design of inhibitors of the aspartic protease endothiapepsin by exploiting dynamic combinatorial chemistry.
Authors: Mondal, M. / Radeva, N. / Koster, H. / Park, A. / Potamitis, C. / Zervou, M. / Klebe, G. / Hirsch, A.K.
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)34,88311
Polymers33,8141
Non-polymers1,06910
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.467, 73.104, 53.134
Angle α, β, γ (deg.)90.00, 109.61, 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 , 5 types, 343 molecules

#2: Chemical ChemComp-1TZ / (2S)-2-azanyl-3-(3H-indol-3-yl)-N-[(E)-(2,4,6-trimethylphenyl)methylideneamino]propanamide / (2S)-2-amino-3-(1H-indol-3-yl)-N-[(E)-(2,4,6-trimethylphenyl)methyleneamino]propanamide


Mass: 348.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N4O
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2M ammonium acetate, 1m sodium acetate, 50% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2013 / Details: mirrors
RadiationMonochromator: Si-111 Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. all: 34335 / Num. obs: 34335 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.084 / Net I/σ(I): 17.4
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1708 / Rsym value: 0.485 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PCW

3pcw


Resolution: 1.73→26.312 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.86 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1756 1734 5.05 %random
Rwork0.1462 ---
obs0.1478 34317 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→26.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 70 333 2772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062532
X-RAY DIFFRACTIONf_angle_d1.0283469
X-RAY DIFFRACTIONf_dihedral_angle_d10.261814
X-RAY DIFFRACTIONf_chiral_restr0.069406
X-RAY DIFFRACTIONf_plane_restr0.004442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.77680.26571380.19022615X-RAY DIFFRACTION97
1.7768-1.83410.18871560.17272685X-RAY DIFFRACTION99
1.8341-1.89970.20281610.15432707X-RAY DIFFRACTION100
1.8997-1.97570.18761330.14512721X-RAY DIFFRACTION100
1.9757-2.06560.17771440.13462703X-RAY DIFFRACTION100
2.0656-2.17440.17481260.12762722X-RAY DIFFRACTION100
2.1744-2.31060.16151340.13592755X-RAY DIFFRACTION100
2.3106-2.48890.19041500.14372680X-RAY DIFFRACTION100
2.4889-2.73910.16521510.14952744X-RAY DIFFRACTION100
2.7391-3.13490.18621360.14652737X-RAY DIFFRACTION100
3.1349-3.94750.15341550.13742722X-RAY DIFFRACTION100
3.9475-26.31510.16751500.15342792X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42260.0622-0.00670.65450.03791.3773-0.0253-0.08640.04110.1016-0.0153-0.0177-0.0412-0.05060.03810.09950.011-0.00570.0756-0.0020.086733.0666-5.314364.5961
21.6562-0.09140.53610.5734-0.20130.6498-0.01220.02640.03490.0117-0.0226-0.0564-0.03710.00340.0380.08260.00090.01920.05370.00120.070929.73387.513844.9046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 183 )
2X-RAY DIFFRACTION2chain 'A' and (resid 184 through 330 )

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