1DZM

Porcine Odorant Binding Protein Complexed with benzoic acid phenylmethylester


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1006/jmbi.2000.3820
  • Primary Citation of Related Structures:  1DZJ, 1DZK, 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ODORANT-BINDING PROTEIN
A, B
157Sus scrofaN/A
Find proteins for P81245 (Sus scrofa)
Go to UniProtKB:  P81245
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BZM
Query on BZM

Download SDF File 
Download CCD File 
A, B
BENZOIC ACID PHENYLMETHYLESTER
C14 H12 O2
SESFRYSPDFLNCH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BZMIC50: 3900 nM BINDINGMOAD
BZMIC50: 3900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.009α = 90.00
b = 88.679β = 90.00
c = 93.163γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-06
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance