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- PDB-2jji: Endothiapepsin in complex with a gem-diol inhibitor. -

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Basic information

Entry
Database: PDB / ID: 2jji
TitleEndothiapepsin in complex with a gem-diol inhibitor.
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / ASPARTYL PROTEASE / ZYMOGEN / 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
GEM-DIOL INHIBITOR PD-135.040 / Chem-0QS / Endothiapepsin
Similarity search - Component
Biological speciesCRYPHONECTRIA PARASITICA (chestnut blight fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsCoates, L. / Tuan, H.-F. / Tomanicek, S.J. / Kovalevsky, A. / Mustyakimov, M. / Erskine, P. / Cooper, J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2008
Title: The Catalytic Mechanism of an Aspartic Proteinase Explored with Neutron and X-Ray Diffraction
Authors: Coates, L. / Tuan, H.-F. / Tomanicek, S.J. / Kovalevsky, A. / Mustyakimov, M. / Erskine, P. / Cooper, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Preliminary Neutron and Ultrahigh-Resolution X-Ray Diffraction Studies of the Aspartic Proteinase Endothiapepsin Cocrystallized with a Gem-Diol Inhibitor.
Authors: Tuan, H.-F. / Erskine, P. / Langan, P. / Cooper, J. / Coates, L.
History
DepositionApr 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Mar 6, 2013Group: Other
Revision 1.3Sep 25, 2013Group: Database references / Other
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.5May 22, 2019Group: Data collection / Derived calculations / Refinement description
Category: refine / struct_conn
Item: _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_rmsd_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOTHIAPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6773
Polymers33,7961
Non-polymers8812
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.030, 75.720, 42.970
Angle α, β, γ (deg.)90.00, 97.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOTHIAPEPSIN / / ASPARTATE PROTEASE


Mass: 33795.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ENDOTHIA PARASITICA
Source: (natural) CRYPHONECTRIA PARASITICA (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Chemical ChemComp-0QS / N~2~-[(2R)-2-benzyl-3-(tert-butylsulfonyl)propanoyl]-N-{(1R)-1-(cyclohexylmethyl)-3,3-difluoro-2,2-dihydroxy-4-[(2-morpholin-4-ylethyl)amino]-4-oxobutyl}-3-(1H-imidazol-3-ium-4-yl)-L-alaninamide / PD-135,040


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 784.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56F2N7O8S / References: GEM-DIOL INHIBITOR PD-135.040
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.38 Å3/Da / Density % sol: 37.84 % / Description: NONE

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Site: ESRF / Beamline: ID29 / Type: BRUKER / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.56→18.24 Å / Num. obs: 289999 / % possible obs: 94.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.7
Reflection shellResolution: 1.56→1.65 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.4 / % possible all: 82.9

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Processing

SoftwareName: SHELXL-97 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→30 Å / Num. parameters: 10912 / Num. restraintsaints: 10312 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1826 5.3 %RANDOM
all0.156 34727 --
obs0.157 -90.5 %-
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 2276 / Occupancy sum non hydrogen: 2711
Refinement stepCycle: LAST / Resolution: 1.57→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 59 264 2711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.033
X-RAY DIFFRACTIONs_angle_d0.048
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.179
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.094
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0

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