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- PDB-1epr: ENDOTHIA ASPARTIC PROTEINASE (ENDOTHIAPEPSIN) COMPLEXED WITH PD-1... -

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Basic information

Entry
Database: PDB / ID: 1epr
TitleENDOTHIA ASPARTIC PROTEINASE (ENDOTHIAPEPSIN) COMPLEXED WITH PD-135,040
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / ACID PROTEINASE
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 / Resolution: 2.3 Å
AuthorsBadasso, M. / Crawford, M. / Cooper, J.B. / Blundell, T.L.
Citation
Journal: Protein Sci. / Year: 1994
Title: A structural comparison of 21 inhibitor complexes of the aspartic proteinase from Endothia parasitica.
Authors: Bailey, D. / Cooper, J.B.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: The 3D Structure at 2 Angstroms Resolution of Endothiapepsin
Authors: Blundell, T.L. / Jenkins, J. / Sewell, B.T. / Pearl, L.H. / Cooper, J.B. / Tickle, I.J. / Veerapandian, B. / Wood, S.P.
History
DepositionJul 27, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: ENDOTHIAPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5992
Polymers33,8141
Non-polymers7851
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.090, 75.770, 43.010
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: THR E 22 - PRO E 23 OMEGA = 293.30 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: SER E 132 - PRO E 133 OMEGA = 30.48 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: GLN E 134A - GLN E 135 OMEGA = 80.17 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein ENDOTHIAPEPSIN /


Mass: 33813.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 63A, 80A, 134A, 184A, 203A, 204A, 238A, 282A, 282B, AND 319A IN CHAIN E ARE INSERTIONS ...RESIDUES 63A, 80A, 134A, 184A, 203A, 204A, 238A, 282A, 282B, AND 319A IN CHAIN E ARE INSERTIONS RELATIVE TO PORCINE PEPSIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.3 Å

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementResolution: 2.3→12 Å / σ(F): 3
Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE ...Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION: B = 8 * (PI)**2 * U**2. THERE ARE ARE LARGE NUMBER OF CLOSE ATOMIC INTERACTIONS, SOME AMONG ATOMS WITHIN THE ENTRY AND OTHERS BETWEEN ATOMS WITHIN THE ENTRY AND SYMMETRY-RELATED ENTRIES.
RfactorNum. reflection% reflection
obs0.181 13462 99.7 %
Refinement stepCycle: LAST / Resolution: 2.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 54 346 2789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d0.019
X-RAY DIFFRACTIONp_planar_d0.0001
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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