Oligopeptidase B from Trypanosoma brucei with covalently bound antipain - closed form

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

This is version 3.0 of the entry. See complete history


Crystal Structures of Trypanosoma Brucei Oligopeptidase B Broaden the Paradigm of Catalytic Regulation in Prolyl Oligopeptidase Family Enzymes.

Canning, P.Rea, D.Morty, R.E.Fulop, V.

(2013) PLoS One 8: 79349

  • DOI: https://doi.org/10.1371/journal.pone.0079349
  • Primary Citation of Related Structures:  
    4BP8, 4BP9

  • PubMed Abstract: 

    Oligopeptidase B cleaves after basic amino acids in peptides up to 30 residues. As a virulence factor in bacteria and trypanosomatid pathogens that is absent in higher eukaryotes, this is a promising drug target. Here we present ligand-free open state and inhibitor-bound closed state crystal structures of oligopeptidase B from Trypanosoma brucei, the causative agent of African sleeping sickness. These (and related) structures show the importance of structural dynamics, governed by a fine enthalpic and entropic balance, in substrate size selectivity and catalysis. Peptides over 30 residues cannot fit the enzyme cavity, preventing the complete domain closure required for a key propeller Asp/Glu to fix the catalytic His and Arg in the catalytically competent conformation. This size exclusion mechanism protects larger peptides and proteins from degradation. Similar bacterial prolyl endopeptidase and archael acylaminoacyl peptidase structures demonstrate this mechanism is conserved among oligopeptidase family enzymes across all three domains of life.

  • Organizational Affiliation

    School of Life Sciences, University of Warwick, Coventry, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
715Trypanosoma bruceiMutation(s): 0 
Find proteins for O76728 (Trypanosoma brucei brucei)
Explore O76728 
Go to UniProtKB:  O76728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76728
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
G, H, I, J, K
G, H, I, J, K, L
4ActinomycetesMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on OAR
G, H, I, J, K
G, H, I, J, K, L
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.8α = 90
b = 148.8β = 91
c = 268γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Atomic model, Database references
  • Version 1.2: 2014-06-18
    Changes: Atomic model
  • Version 1.3: 2017-09-13
    Changes: Advisory, Derived calculations
  • Version 2.0: 2019-05-15
    Changes: Advisory, Data collection, Derived calculations, Polymer sequence
  • Version 2.1: 2019-07-10
    Changes: Data collection
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other