Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

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This is version 2.0 of the entry. See complete history


Structures of Prolyl Oligopeptidase Substrate/ Inhibitor Complexes. Use of Inhibitor Binding for Titration of the Catalytic Histidine Residue

Fulop, V.Szeltner, Z.Renner, V.Polgar, L.

(2001) J Biol Chem 276: 1262

  • DOI: https://doi.org/10.1074/jbc.M007003200
  • Primary Citation of Related Structures:  
    1E8M, 1E8N

  • PubMed Abstract: 

    Structure determination of the inactive S554A variant of prolyl oligopeptidase complexed with an octapeptide has shown that substrate binding is restricted to the P4-P2' region. In addition, it has revealed a hydrogen bond network of potential catalytic importance not detected in other serine peptidases. This involves a unique intramolecular hydrogen bond between the P1' amide and P2 carbonyl groups and another between the P2' amide and Nepsilon2 of the catalytic histidine 680 residue. It is argued that both hydrogen bonds promote proton transfer from the imidazolium ion to the leaving group. Another complex formed with the product-like inhibitor benzyloxycarbonyl-glycyl-proline, indicating that the carboxyl group of the inhibitor forms a hydrogen bond with the Nepsilon2 of His(680). Because a protonated histidine makes a stronger interaction with the carboxyl group, it offers a possibility of the determination of the real pK(a) of the catalytic histidine residue. This was found to be 6.25, lower than that of the well studied serine proteases. The new titration method gave a single pK(a) for prolyl oligopeptidase, whose reaction exhibited a complex pH dependence for k(cat)/K(m), and indicated that the observed pK(a) values are apparent. The procedure presented may be applicable for other serine peptidases.

  • Organizational Affiliation

    Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROLYL ENDOPEPTIDASE710Sus scrofaMutation(s): 1 
Gene Names: PREP
Find proteins for P23687 (Sus scrofa)
Explore P23687 
Go to UniProtKB:  P23687
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23687
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDE INHIBITORB [auth I]9synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.7α = 90
b = 99.7β = 90
c = 110.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2001-01-16 
  • Deposition Author(s): Fulop, V.

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2016-12-28
    Changes: Source and taxonomy
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations