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- PDB-3pgi: Endothiapepsin in complex with a fragment -

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Basic information

Entry
Database: PDB / ID: 3pgi
TitleEndothiapepsin in complex with a fragment
ComponentsEndothiapepsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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-F41 / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKoester, H. / Heine, A. / Klebe, G.
CitationJournal: 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: Koster, H. / Craan, T. / Brass, S. / Herhaus, C. / Zentgraf, M. / Neumann, L. / Heine, A. / Klebe, G.
History
DepositionNov 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Sep 6, 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
Revision 1.5Oct 9, 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)34,1683
Polymers33,8141
Non-polymers3542
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.340, 72.810, 52.820
Angle α, β, γ (deg.)90.00, 109.62, 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-F41 / N-(1,3-benzodioxol-5-yl)-2-(piperidin-1-yl)acetamide


Mass: 262.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N2O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M NH4Ac, 0.1M Acetate Buffer, 26% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K, temperature 289K, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2010
RadiationMonochromator: collimating morrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 25348 / Num. obs: 25348 / % possible obs: 100 % / Redundancy: 3.6 % / Rsym value: 0.065 / Net I/σ(I): 26.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 1213 / Rsym value: 0.287 / % possible all: 100

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OEW

1oew


Resolution: 1.9→10 Å / Num. parameters: 10515 / Num. restraintsaints: 9989 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 1194 -RANDOM
Rwork0.1618 ---
all0.1632 23371 --
obs-23371 92.1 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2229 / Occupancy sum non hydrogen: 2625
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 25 239 2625
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0273
X-RAY DIFFRACTIONs_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0

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