Aspartyl Dipeptidase

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.218 

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This is version 1.4 of the entry. See complete history


The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad.

Hakansson, K.Wang, A.H.Miller, C.G.

(2000) Proc Natl Acad Sci U S A 97: 14097-14102

  • DOI: https://doi.org/10.1073/pnas.260376797
  • Primary Citation of Related Structures:  
    1FY2, 1FYE

  • PubMed Abstract: 

    The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E, was solved crystallographically and refined to 1.2-A resolution. The structure of this 25-kDa enzyme consists of two mixed beta-sheets forming a V, flanked by six alpha-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organization of the catalytic triad differ from those of the known serine proteases. This enzyme is a member of a family of serine hydrolases and appears to represent a new example of convergent evolution of peptidase activity.

  • Organizational Affiliation

    Departments of Microbiology and Cell and Structural Biology, B103 Chemical and Life Science Laboratory, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ASPARTYL DIPEPTIDASE229Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
EC: 3.4
Find proteins for P36936 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P36936 
Go to UniProtKB:  P36936
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36936
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CD

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.986α = 90
b = 42.69β = 106.06
c = 62.496γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-10
    Type: Initial release
  • Version 1.1: 2007-10-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations