2AVI

THREE-DIMENSIONAL STRUCTURES OF AVIDIN AND THE AVIDIN-BIOTIN COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.151 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Three-dimensional structures of avidin and the avidin-biotin complex.

Livnah, O.Bayer, E.A.Wilchek, M.Sussman, J.L.

(1993) Proc Natl Acad Sci U S A 90: 5076-5080

  • DOI: 10.1073/pnas.90.11.5076
  • Primary Citation of Related Structures:  
    2AVI

  • PubMed Abstract: 
  • The crystal structures of a deglycosylated form of the egg-white glycoprotein avidin and of its complex with biotin have been determined to 2.6 and 3.0 A, respectively. The structures reveal the amino acid residues critical for stabilization of the tetrameric assembly and for the exceptionally tight binding of biotin ...

    The crystal structures of a deglycosylated form of the egg-white glycoprotein avidin and of its complex with biotin have been determined to 2.6 and 3.0 A, respectively. The structures reveal the amino acid residues critical for stabilization of the tetrameric assembly and for the exceptionally tight binding of biotin. Each monomer is an eight-stranded antiparallel beta-barrel, remarkably similar to that of the genetically distinct bacterial analog streptavidin. As in streptavidin, binding of biotin involves a highly stabilized network of polar and hydrophobic interactions. There are, however, some differences. The presence of additional hydrophobic and hydrophilic groups in the binding site of avidin (which are missing in streptavidin) may account for its higher affinity constant. Two amino acid substitutions are proposed to be responsible for its susceptibility to denaturation relative to streptavidin. Unexpectedly, a residual N-acetylglucosamine moiety was detected in the deglycosylated avidin monomer by difference Fourier synthesis.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AVIDINA, B128Gallus gallusMutation(s): 0 
Gene Names: AVD
UniProt
Find proteins for P02701 (Gallus gallus)
Explore P02701 
Go to UniProtKB:  P02701
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTN (Subject of Investigation/LOI)
Query on BTN

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BTN PDBBind:  2AVI Kd: 6.00e-7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.151 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.15α = 90
b = 80.37β = 90
c = 43.54γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary