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

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Basic information

Entry
Database: PDB / ID: 1epq
TitleENDOTHIA ASPARTIC PROTEINASE (ENDOTHIAPEPSIN) COMPLEXED WITH PD-133,450 (SOT PHE GLY+SCC GCL)
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
N-[(1S)-2-{[(2S,3R,4S)-1-cyclohexyl-3,4-dihydroxy-6-methylheptan-2-yl]amino}-1-(ethylsulfanyl)-2-oxoethyl]-Nalpha-(morpholin-4-ylsulfonyl)-L-phenylalaninamide / Chem-0QF / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsDealwis, C. / Cooper, J.B. / Blundell, T.L.
Citation
Journal: J.Med.Chem. / Year: 1993
Title: Analyses of ligand binding in five endothiapepsin crystal complexes and their use in the design and evaluation of novel renin inhibitors.
Authors: Lunney, E.A. / Hamilton, H.W. / Hodges, J.C. / Kaltenbronn, J.S. / Repine, J.T. / Badasso, M. / Cooper, J.B. / Dealwis, C. / Wallace, B.A. / Lowther, W.T.
#1: Journal: To be Published
Title: A Structural Comparison of 21 Inhibitor Complexes of the Aspartic Proteinase from Endothia Parasitica
Authors: Bailey, D. / Cooper, J.B.
#2: 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 1.1May 22, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5May 27, 2020Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.6Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification / _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
E: ENDOTHIAPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6634
Polymers33,8141
Non-polymers8493
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.100, 75.700, 42.900
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO E 23 / 2: CIS PROLINE - PRO E 133

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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-0QF / N-[(1S)-2-{[(2S,3R,4S)-1-cyclohexyl-3,4-dihydroxy-6-methylheptan-2-yl]amino}-1-(ethylsulfanyl)-2-oxoethyl]-Nalpha-(morp holin-4-ylsulfonyl)-L-phenylalaninamide / PD-133,450


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 656.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H52N4O7S2
References: N-[(1S)-2-{[(2S,3R,4S)-1-cyclohexyl-3,4-dihydroxy-6-methylheptan-2-yl]amino}-1-(ethylsulfanyl)-2-oxoethyl]-Nalpha-(morpholin-4-ylsulfonyl)-L-phenylalaninamide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE INHIBITOR HAS A K(I) OF 6 NM FOR ENDOTHIAPEPSIN.
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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal grow
*PLUS
Method: unknown / PH range low: 6.3 / PH range high: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.2 Mammonium sulfate11
20.1 Msodium dihydrogen11
3acetate11can be replaced with phosphate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 19853 / % possible obs: 94 % / Rmerge(I) obs: 0.051

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementResolution: 1.9→20 Å / σ(F): 0
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.
RfactorNum. reflection% reflection
obs0.17 19853 88.5 %
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 48 263 2700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.019
X-RAY DIFFRACTIONp_planar_d0.001
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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