1GT1

Complex of Bovine Odorant Binding Protein with Aminoanthracene and pyrazine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of Bovine Odorant-Binding Protein in Complex with Odorant Molecules.

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

(2004) Eur J Biochem 271: 3832

  • DOI: 10.1111/j.1432-1033.2004.04315.x
  • Primary Citation of Related Structures:  
    1GT5, 1GT4, 1GT3, 1GT1

  • PubMed Abstract: 
  • The structure of bovine odorant-binding protein (bOBP) revealed a striking feature of a dimer formed by domain swapping [Tegoni, M., Ramoni, R., Bignetti, E., Spinelli, S. & Cambillau, C. (1996) Nat. Struct. Biol.3, 863-867; Bianchet, M.A., Bains, G., Pelosi, P ...

    The structure of bovine odorant-binding protein (bOBP) revealed a striking feature of a dimer formed by domain swapping [Tegoni, M., Ramoni, R., Bignetti, E., Spinelli, S. & Cambillau, C. (1996) Nat. Struct. Biol.3, 863-867; Bianchet, M.A., Bains, G., Pelosi, P., Pevsner, J., Snyder, S.H., Monaco, H.L. & Amzel, L.M. (1996) Nat. Struct. Biol.3, 934-939] and the presence of a naturally occuring ligand [Ramoni, R., Vincent, F., Grolli, S., Conti, V., Malosse, C., Boyer, F.D., Nagnan-Le Meillour, P., Spinelli, S., Cambillau, C. & Tegoni, M. (2001) J. Biol. Chem.276, 7150-7155]. These features led us to investigate the binding of odorant molecules with bOBP in solution and in the crystal. The behavior of odorant molecules in bOBP resembles that observed with porcine OBP (pOBP), although the latter is monomeric and devoid of ligand when purified. The odorant molecules presented K(d) values with bOBP in the micromolar range. Most of the X-ray structures revealed that odorant molecules interact with a common set of residues forming the cavity wall and do not exhibit specific interactions. Depending on the ligand and on the monomer (A or B), a single residue--Phe89--presents alternate conformations and might control cross-talking between the subunits. Crystal data on both pOBP and bOBP, in contrast with binding and spectroscopic studies on rat OBP in solution, reveal an absence of significant conformational changes involving protein loops or backbone. Thus, the role of OBP in signal triggering remains unresolved.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS, 13402 Marseille, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ODORANT-BINDING PROTEIN AB159Bos taurusMutation(s): 0 
Find proteins for P07435 (Bos taurus)
Explore P07435 
Go to UniProtKB:  P07435
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANC
Query on ANC

Download Ideal Coordinates CCD File 
A, B
ANTHRACEN-1-YLAMINE
C14 H11 N
YUENFNPLGJCNRB-UHFFFAOYSA-N
 Ligand Interaction
PRZ
Query on PRZ

Download Ideal Coordinates CCD File 
A
2-ISOBUTYL-3-METHOXYPYRAZINE
C9 H14 N2 O
UXFSPRAGHGMRSQ-UHFFFAOYSA-N
 Ligand Interaction
3OM
Query on 3OM

Download Ideal Coordinates CCD File 
B
(3S)-1-octen-3-ol
C8 H16 O
VSMOENVRRABVKN-MRVPVSSYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ANCKd :  1000   nM  PDBBind
ANCKd:  1000   nM  Binding MOAD
3OMKd:  1200   nM  Binding MOAD
PRZKd:  3300   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.589α = 90
b = 65.206β = 98.32
c = 42.153γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-03
    Type: Initial release
  • Version 1.1: 2011-12-14
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2014-02-26
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Source and taxonomy
  • Version 1.3: 2015-04-15
    Changes: Database references