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 

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:  1GT3, 1GT4, 1GT5

  • 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. ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ODORANT-BINDING PROTEIN
A, B
159Bos taurusN/A
Find proteins for P07435 (Bos taurus)
Go to UniProtKB:  P07435
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3OM
Query on 3OM

Download SDF File 
Download CCD File 
B
(3S)-1-octen-3-ol
C8 H16 O
VSMOENVRRABVKN-MRVPVSSYSA-N
 Ligand Interaction
PRZ
Query on PRZ

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

Download SDF File 
Download CCD File 
A, B
ANTHRACEN-1-YLAMINE
AMINOANTHRACENE
C14 H11 N
YUENFNPLGJCNRB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3OMKd: 1200 nM BINDINGMOAD
ANCKd: 1000 nM BINDINGMOAD
PRZKd: 3300 nM BINDINGMOAD
ANCKd: 1000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.589α = 90.00
b = 65.206β = 98.32
c = 42.153γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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