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 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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:  
    1E02, 1E00, 1E06, 1DZM, 1DZK, 1DZJ, 1DZP

  • 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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ODORANT-BINDING PROTEINA, B157Sus scrofaMutation(s): 0 
UniProt
Find proteins for P81245 (Sus scrofa)
Explore P81245 
Go to UniProtKB:  P81245
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BZM (Subject of Investigation/LOI)
Query on BZM

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]BENZOIC ACID PHENYLMETHYLESTER
C14 H12 O2
SESFRYSPDFLNCH-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BZM Binding MOAD:  1DZM IC50: 3900 (nM) from 1 assay(s)
PDBBind:  1DZM IC50: 3900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.009α = 90
b = 88.679β = 90
c = 93.163γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

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: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Advisory, Data collection, Experimental preparation, Other