Porcine Odorant Binding Protein Complexed with 2-amino-4-butyl-5-propylselenazole

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Complexes of Porcine Odorant Binding Protein with Odorant Molecules Belonging to Different Chemical Classes

Vincent, F.Spinelli, S.Ramoni, R.Grolli, S.Pelosi, P.Cambillau, C.Tegoni, M.

(2000) J Mol Biol 300: 127

  • DOI: https://doi.org/10.1006/jmbi.2000.3820
  • Primary Citation of Related Structures:  
    1DZJ, 1DZK, 1DZM, 1DZP, 1E00, 1E02, 1E06

  • PubMed Abstract: 

    Porcine odorant binding protein (pOBP) is a monomer of 157 amino acid residues, purified in abundance from pig nasal mucosa. In contrast to the observation on lipocalins as retinol binding protein (RBP), major urinary protein (MUP) or bovine odorant binding protein (bOBP), no naturally occurring ligand was found in the beta-barrel cavity of pOBP. Porcine OBP was therefore chosen as a simple model for structure/function studies with odorant molecules. In competition experiments with tritiated pyrazine, the affinity of pOBP towards several odorant molecules belonging to different chemical classes has been found to be of the micromolar order, with a 1:1 stoichiometry. The X-ray structures of pOBP complexed to these molecules were determined at resolution between 2.15 and 1.4 A. As expected, the electron density of the odorant molecules was observed into the hydrophobic beta-barrel of the lipocalin. Inside this cavity, very few specific interactions were established between the odorant molecule and the amino acid side-chains, which did not undergo significant conformational change. The high B-factors observed for the odorant molecules as well as the existence of alternative conformations reveal a non-specific mode of binding of the odorant molecules in the cavity.

  • Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, URA 9039, CNRS, IFR1, 31 Chemin Joseph Aiguier, Marseille, Cedex 20, 13402, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
157Sus scrofaMutation(s): 0 
Find proteins for P81245 (Sus scrofa)
Explore P81245 
Go to UniProtKB:  P81245
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81245
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SES

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C10 H18 N2 Se
Binding Affinity Annotations 
IDSourceBinding Affinity
SES Binding MOAD:  1DZJ IC50: 1300 (nM) from 1 assay(s)
PDBBind:  1DZJ IC50: 1300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.362α = 90
b = 88.739β = 90
c = 93.197γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Advisory, Data collection, Experimental preparation, Other