1VYG

schistosoma mansoni fatty acid binding protein in complex with arachidonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Schistosoma Mansoni Fatty Acid Binding Protein: Specificity and Functional Control as Revealed by Crystallographic Structure

Angelucci, F.Johnson, K.A.Baiocco, P.Miele, A.E.Brunori, M.Valle, C.Vigorosi, F.Troiani, A.R.Liberti, P.Cioli, D.Klinkert, M.Q.Bellelli, A.

(2004) Biochemistry 43: 13000

  • DOI: https://doi.org/10.1021/bi048505f
  • Primary Citation of Related Structures:  
    1VYF, 1VYG

  • PubMed Abstract: 

    Schistosoma mansoni fatty acid binding protein (Sm14) was crystallized with bound oleic acid (OLA) and arachidonic acid (ACD), and their structures were solved at 1.85 and 2.4 A resolution, respectively. Sm14 is a vaccine target for schistosomiasis, the second most prevalent parasitic disease in humans. The parasite is unable to synthesize fatty acids depending on the host for these nutrients. Moreover, arachidonic acid (ACD) is required to synthesize prostaglandins employed by schistosomes to evade the host's immune defenses. In the complex, the hydrocarbon tail of bound OLA assumes two conformations, whereas ACD adopts a unique hairpin-looped structure. ACD establishes more specific interactions with the protein, among which the most important is a pi-cation bond between Arg78 and the double bond at C8. Comparison with homologous fatty acid binding proteins suggests that the binding site of Sm14 is optimized to fit ACD. To test the functional implications of our structural data, the affinity of Sm14 for 1,8-anilinonaphthalenesulfonic acid (ANS) has been measured; moreover the binding constants of six different fatty acids were determined from their ability to displace ANS. OLA and ACD exhibited the highest affinities. To determine the rates of fatty acid binding and dissociation we carried out stopped flow kinetic experiments monitoring displacement by (and of) ANS. The binding rate constant of ligands is controlled by a slow pH dependent conformational change, which we propose to have physiological relevance.


  • Organizational Affiliation

    Department of Biochemical Sciences A. Rossi Fanelli, CNR Institute of Molecular Biology and Pathology and Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FATTY ACID BINDING PROTEIN135Schistosoma mansoniMutation(s): 0 
UniProt
Find proteins for P29498 (Schistosoma mansoni)
Explore P29498 
Go to UniProtKB:  P29498
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29498
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACD
Query on ACD

Download Ideal Coordinates CCD File 
B [auth A]ARACHIDONIC ACID
C20 H32 O2
YZXBAPSDXZZRGB-DOFZRALJSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ACD PDBBind:  1VYG Kd: 10 (nM) from 1 assay(s)
Binding MOAD:  1VYG Kd: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.29α = 90
b = 91.01β = 90
c = 35.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description