1VYO

Crystal structure of avidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding Properties of Haba-Type Azo Derivatives to Avidin and Avidin-Related Protein 4.

Repo, S.Paldanius, T.A.Hytonen, V.P.Nyholm, T.K.Halling, K.K.Huuskonen, J.Pentikainen, O.T.Rissanen, K.Slotte, J.P.Airenne, T.T.Salminen, T.A.Kulomaa, M.S.Johnson, M.S.

(2006) Chem.Biol. 13: 1029

  • DOI: 10.1016/j.chembiol.2006.08.006

  • PubMed Abstract: 
  • The chicken genome encodes several biotin-binding proteins, including avidin and avidin-related protein 4 (AVR4). In addition to D-biotin, avidin binds an azo dye compound, 4-hydroxyazobenzene-2-carboxylic acid (HABA), but the HABA-binding properties ...

    The chicken genome encodes several biotin-binding proteins, including avidin and avidin-related protein 4 (AVR4). In addition to D-biotin, avidin binds an azo dye compound, 4-hydroxyazobenzene-2-carboxylic acid (HABA), but the HABA-binding properties of AVR4 are not yet known. Differential scanning calorimetry, UV/visible spectroscopy, and molecular modeling were used to analyze the binding of 15 azo molecules to avidin and AVR4. Significant differences are seen in azo compound preferences for the two proteins, emphasizing the importance of the loop between strands beta3 and beta4 for azo ligand recognition; information on these loops is provided by the high-resolution (1.5 A) X-ray structure for avidin reported here. These results may be valuable in designing improved tools for avidin-based life science and nanobiotechnology applications.


    Organizational Affiliation

    Department of Biochemistry and Pharmacy, Abo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AVIDIN
A, B
128Gallus gallusMutation(s): 0 
Gene Names: AVD
Find proteins for P02701 (Gallus gallus)
Go to UniProtKB:  P02701
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.949α = 90.00
b = 78.772β = 90.00
c = 43.010γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance