2ER6

The structure of a synthetic pepsin inhibitor complexed with endothiapepsin.

• PDB DOI: https://doi.org/10.2210/pdb2ER6/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Cryphonectria parasitica
• Mutation(s): No 


• Deposited: 1990-10-13 Released: 1991-01-15 
• Deposition Author(s): Cooper, J.B., Foundling, S.I., Szelke, M., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.200 

Literature

The structure of a synthetic pepsin inhibitor complexed with endothiapepsin

Cooper, J., Foundling, S., Hemmings, A., Blundell, T., Jones, D.M., Hallett, A., Szelke, M.

(1987) Eur J Biochem 169: 215-221

• PubMed: 3119339 
• DOI: https://doi.org/10.1111/j.1432-1033.1987.tb13600.x
• Primary Citation of Related Structures:  
  2ER6


• PubMed Abstract: 
  

  The conformation of a synthetic polypeptide inhibitor, bound to the active site of the fungal aspartic proteinase endothiapepsin (EC 3.4.23.6), has been determined by X-ray diffraction at 0.20-nm resolution and refined to an agreement factor of 0.20. The inhibitor: Pro Thr Glu Phe-R-Phe Arg Glu (R = -CH2NH-) is based on a chromogenic substrate of pepsin (EC 3.4.23.1). It has, in place of the scissile bond, a reduced peptide group which is resistant to hydrolysis and mimics the tetrahedral transition state. The inhibitor binds in an extended conformation with the reduced bond close to the essential aspartate side-chains of the enzyme. The hydrogen bonds and hydrophobic interactions between the enzyme and the inhibitor do not induce large conformational changes.

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Organizational Affiliation: 

Department of Crystallography, Birkbeck College, London, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.73 kDa 
• Atom Count: 2,775 
• Modelled Residue Count: 336 
• Deposited Residue Count: 336 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOTHIAPEPSIN	A [auth E]	330	Cryphonectria parasitica	Mutation(s): 0  EC: 3.4.23.6 (PDB Primary Data), 3.4.23.22 (UniProt)
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838  Go to UniProtKB:  P11838

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H-256 peptide	B [auth I]	6	N/A	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000346	B [auth I]	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	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.4	α = 90
b = 73.8	β = 109.5
c = 45.6	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-01-15 
Deposition Author(s): Cooper, J.B., Foundling, S.I., Szelke, M., Blundell, T.L.

Revision History  

• Version 1.0: 1991-01-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-11-20
  Changes: Structure summary