2ERB | pdb_00002erb

AgamOBP1, and odorant binding protein from Anopheles gambiae complexed with PEG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.204 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

The crystal structure of an odorant binding protein from Anopheles gambiae: Evidence for a common ligand release mechanism.

Wogulis, M.Morgan, T.Ishida, Y.Leal, W.S.Wilson, D.K.

(2006) Biochem Biophys Res Commun 339: 157-164

  • DOI: https://doi.org/10.1016/j.bbrc.2005.10.191
  • Primary Citation Related Structures: 
    2ERB

  • PubMed Abstract: 

    The Anopheles gambiae mosquito is the main vector of malaria transmission in sub-Saharan Africa. We present here a 1.5A crystal structure of AgamOBP1, an odorant binding protein (OBP) from the A. gambiae mosquito. The protein crystallized as a dimer with a unique binding pocket consisting of a continuous tunnel running through both subunits of the dimer and occupied by a PEG molecule. We demonstrate that AgamOBP1 undergoes a pH dependent conformational change that is associated with reduced ligand binding. A predominance of acid-labile hydrogen bonds involving the C-terminal loop suggests a mechanism in which a drop in pH causes C-terminal loop to open, leaving the binding tunnel solvent exposed, thereby lowering binding affinity for ligand. Because proteins from two distantly related insects also undergo a pH dependent conformational change involving the C-terminus that is associated with reduced ligand affinity, our results suggest a common mechanism for OBP activity.


  • Organizational Affiliation
    • Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.

Macromolecule Content 

  • Total Structure Weight: 30.34 kDa 
  • Atom Count: 2,530 
  • Modeled Residue Count: 246 
  • Deposited Residue Count: 250 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
odorant binding protein
A, B
125Anopheles gambiaeMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEU

Query on PEU



Download:Ideal Coordinates CCD File
D [auth B]2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
C55 H112 O28
ISGUIIHZEJGUGQ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.204 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.1α = 90
b = 68.21β = 99.77
c = 61.48γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary