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- PDB-1od1: Endothiapepsin PD135,040 complex -

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Basic information

Entry
Database: PDB / ID: 1od1
TitleEndothiapepsin PD135,040 complex
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / INHIBITOR / ASPARTYL 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
GEM-DIOL INHIBITOR PD-135.040 / Chem-0QS / Endothiapepsin
Similarity search - Component
Biological speciesCRYPHONECTRIA PARASITICA (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.37 Å
AuthorsCoates, L. / Erskine, P.T. / Mall, S. / Gill, R.S. / Wood, S.P. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: The Structure of Endothiapepsin Complexed with the Gem-Diol Inhibitor Pd-135,040 at 1.37 A
Authors: Coates, L. / Erskine, P.T. / Mall, S. / Williams, P.A. / Gill, R.S. / Wood, S.P. / Cooper, J.B.
History
DepositionFeb 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: 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 1.2Nov 30, 2012Group: Other
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

Downloads & links

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Assembly

Deposited unit
A: ENDOTHIAPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7914
Polymers33,8141
Non-polymers9773
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.201, 73.249, 45.993
Angle α, β, γ (deg.)90.00, 110.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOTHIAPEPSIN / / ASPARTATE PROTEASE / EAPA / EPN-1


Mass: 33813.855 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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYSES PROTEINS WITH BROAD SPECIFICITY LIKE PEPSIN A PREFERRING HYDROPHOBIC RESIDUES AT P1 AND P1'.

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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: 49.46 %
Crystal growpH: 4.6 / Details: PH 4.60
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 mg/mlprotein1droppH4.6
20.1 Msodium acetate1drop
3100 %satammonium solution1reservoir
40.1 Msodium acetate1reservoirpH4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.918056
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 6, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918056 Å / Relative weight: 1
ReflectionResolution: 1.37→10 Å / Num. obs: 68317 / % possible obs: 98.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 3.2
Reflection shellResolution: 1.37→1.44 Å / Redundancy: 4 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 1.7 / % possible all: 95.5
Reflection
*PLUS
Highest resolution: 1.37 Å / Lowest resolution: 10 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.113
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.37→10 Å / Num. parameters: 26565 / Num. restraintsaints: 32311 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.159 3461 5 %5%
obs0.125 -98.3 %-
all-64650 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 16 / Occupancy sum hydrogen: 2287 / Occupancy sum non hydrogen: 2905
Refinement stepCycle: LAST / Resolution: 1.37→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 64 418 2871
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.042
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.051
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.085
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.1534 / Rfactor Rwork: 0.1153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.0293
X-RAY DIFFRACTIONs_chiral_restr0.061

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