Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.88 kDa 
• Atom Count: 4054 
• Residue Count: 484 
• Unique protein chains: 1

5IRW

Crystal structure of avidin in complex with 1-desthiobiotinylpyrene

• DOI: 10.2210/pdb5IRW/pdb

• Classification: biotin binding protein
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2016-03-14 Released: 2016-10-12 
• Deposition Author(s): Strzelczyk, P., Bujacz, G.
• Funding Organization(s): National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.231 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Structural Characterization of the Avidin Interactions with Fluorescent Pyrene-Conjugates: 1-Biotinylpyrene and 1-Desthiobiotinylpyrene.

Strzelczyk, P., Plazuk, D., Zakrzewski, J., Bujacz, G.

(2016) Molecules 21

• PubMed: 27689976 
• DOI: 10.3390/molecules21101270
• Primary Citation of Related Structures:  
  5IRW, 5IRU


• PubMed Abstract: 
  

Avidin is a tetrameric protein that belongs to the calycin superfamily. It has been studied mainly because of its extraordinary affinity to biotin, which led to a wide range of applications based on the avidin-biotin system. In the present study, we report the first crystal structures of avidin in a complex with two novel fluorescent pyrene derivatives: 1-biotinylpyrene (B9P) and 1-desthiobiotinylpyrene (D9P). The crystal structures were solved by molecular replacement using the coordinates of avidin molecule as a starting model and the final models of avidin/B9P and avidin/D9P were refined to resolutions of 2.0 Å and 2.1 Å, respectively. Our data reveal changes in loop conformation as well as in overall fold and quaternary arrangement of the avidin upon the binding of these fluorescent probes. Moreover, the crystal structures allowed analysis of the details of the interactions between the protein and the pyrene derivatives. Structural description of the complexes will contribute to the design of conjugates for expanding the capabilities of avidin-biotin technology.

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Organizational Affiliation: 

Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-924 Łódź, Stefanowskiego 4/10, Poland. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avidin	A, B, C, D	128	Gallus gallus	Mutation(s): 0  Gene Names: AVD
Find proteins for P02701 (Gallus gallus) Explore P02701  Go to UniProtKB:  P02701

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D9P	A, B, C, D	1-desthiobiotinylpyrene C26 H26 N2 O2 GEJQOLRONNVYHQ-KSFYIVLOSA-N
NAG	A, B, C, D	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.231 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.97	α = 90
b = 81.52	β = 90
c = 107.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-03-14 
• Released Date: 2016-10-12 
Deposition Author(s): Strzelczyk, P., Bujacz, G.

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Funding Organization	Location	Grant Number
National Science Centre	Poland	DEC-2013/11/N/ST5/01296
National Science Centre	Poland	DEC-2015/16/T/ST5/00401

Revision History 

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary