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- PDB-2er6: The structure of a synthetic pepsin inhibitor complexed with endo... -

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Basic information

Entry
Database: PDB / ID: 2er6
TitleThe structure of a synthetic pepsin inhibitor complexed with endothiapepsin.
Components
  • ENDOTHIAPEPSIN
  • H-256 peptide
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-{(2R)-3-phenyl-2-[(L-prolyl-L-threonyl-L-alpha-glutamyl)amino]propyl}-L-phenylalanyl-N~5~-[amino(iminio)methyl]- L-ornithyl-L-glutamic acid / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsCooper, J.B. / Foundling, S.I. / Szelke, M. / Blundell, T.L.
Citation
Journal: Eur.J.Biochem. / Year: 1987
Title: The structure of a synthetic pepsin inhibitor complexed with endothiapepsin
Authors: Cooper, J. / Foundling, S. / Hemmings, A. / Blundell, T. / Jones, D.M. / Hallett, A. / Szelke, M.
#1: Journal: FEBS Lett. / Year: 1984
Title: The Active Site of Aspartic Proteinases
Authors: Pearl, L. / Blundell, T.
#2: Journal: Proc.FEBS Meet. / Year: 1979
Title: Active Site of Acid Proteinases
Authors: Blundell, T.L. / Jones, H.B. / Khan, G. / Taylor, G. / Sewell, T.S. / Pearl, L.H. / Wood, S.P.
#3: Journal: Proc.FEBS Meet. / Year: 1979
Title: The Three-Dimensional Structure of Acid Proteinases
Authors: Blundell, T.L. / Jenkins, J.A. / Khan, G. / Roychowdhury, P. / Sewell, T. / Tickle, I.J. / Wood, E.A.
#4: Journal: Biochim.Biophys.Acta / Year: 1979
Title: Four-Fold Structural Repeat in the Acid Proteases
Authors: Blundell, T.L. / Sewell, B.T. / Mclachlan, A.D.
#5: Journal: Nature / Year: 1978
Title: Structural Evidence for Gene Duplication in the Evolution of Acid Proteases
Authors: Tang, J. / James, M.N.G. / Hsu, I.N. / Jenkins, J.A. / Blundell, T.L.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977
Title: Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica
Authors: Subramanian, E. / Swan, I.D.A. / Liu, M. / Davies, D.R. / Jenkins, J.A. / Tickle, I.J. / Blundell, T.L.
#7: Journal: Adv.Exp.Med.Biol. / Year: 1977
Title: X-Ray Analysis and Circular Dichroism of the Acid Protease from Endothia Parasitica and Chymosin
Authors: Jenkins, J. / Tickle, I. / Sewell, T. / Ungaretti, L. / Wollmer, A. / Blundell, T.
History
DepositionOct 13, 1990Processing site: BNL
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: ENDOTHIAPEPSIN
I: H-256 peptide


Theoretical massNumber of molelcules
Total (without water)34,7262
Polymers34,7262
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.400, 73.800, 45.600
Angle α, β, γ (deg.)90.00, 109.50, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO E 23 AND PRO E 133 ARE CIS PROLINES.
2: THE PEPTIDE BOND BETWEEN PHE I 4 AND PHE I 5 HAS BEEN REDUCED TO CH2-NH2.

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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, EC: 3.4.23.6
#2: Protein/peptide H-256 peptide


Type: Peptide-like / Class: Inhibitor / Mass: 912.019 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-{(2R)-3-phenyl-2-[(L-prolyl-L-threonyl-L-alpha-glutamyl)amino]propyl}-L-phenylalanyl-N~5~-[amino(iminio)methyl]- L-ornithyl-L-glutamic acid
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE COMPLETE SEQUENCE WAS DETERMINED BY V. PEDERSEN AS TRYPTIC FRAGMENTS WHICH WERE ALIGNED IN THE ...THE COMPLETE SEQUENCE WAS DETERMINED BY V. PEDERSEN AS TRYPTIC FRAGMENTS WHICH WERE ALIGNED IN THE ELECTRON DENSITY. HOMOLOGY WITH OTHER ASPARTIC PROTEINASES WAS USED TO RESOLVE ALIGNMENT AMBIGUITIES. THE RESIDUE NUMBERING IS BASED ON THAT OF 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal grow
*PLUS
Method: unknown / Details: Moews, P., (1970) J. Mol. Biol., 54, 395. / 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: 2 Å / Lowest resolution: 9999 Å / Num. obs: 19600 / % possible obs: 88 % / Num. measured all: 30000 / Rmerge(I) obs: 0.04

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→20 Å
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. IT IS AN INDICATION OF POSSIBLE ERRORS IN THE REFINEMENT THAT SOME ARE SLIGHTLY NEGATIVE.
RfactorNum. reflection
Rwork0.2 -
obs-19600
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 0 321 2775
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.022
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Rfactor Rwork: 0.2 / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS

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