5CHK | pdb_00005chk

Crystal structure of avidin - HABA complex (hexagonal crystal form)

• PDB DOI: https://doi.org/10.2210/pdb5CHK/pdb

• Classification: GLYCOPROTEIN
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2015-07-10 Released: 2016-03-23 
• Deposition Author(s): Strzelczyk, P., Bujacz, A., Bujacz, G.
• Funding Organization(s): National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and ligand affinity of avidin in the complex with 4-hydroxyazobenzene-2-carboxylic acid

Strzelczyk, P., Bujacz, G.

(2016) J Mol Struct 1109: 232-238

• DOI: https://doi.org/10.1016/j.molstruc.2016.01.013

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.81 kDa 
• Atom Count: 1,029 
• Modeled Residue Count: 121 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avidin	A	128	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P02701 (Gallus gallus) Explore P02701  Go to UniProtKB:  P02701
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
55R	C [auth A]	2-[2-(4-oxocyclohexa-2,5-dien-1-ylidene)hydrazinyl]benzoic acid C13 H10 N2 O3 FBVSMDPNVYJNON-UHFFFAOYSA-N
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.31	α = 90
b = 61.31	β = 90
c = 120.53	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Strzelczyk, P., Bujacz, A., Bujacz, G.

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

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary