4JHQ | pdb_00004jhq

Crystal structure of avidin - 6-(6-biotinamidohexanamido)hexanoylferrocene complex

• PDB DOI: https://doi.org/10.2210/pdb4JHQ/pdb

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


• Deposited: 2013-03-05 Released: 2013-11-20 
• Deposition Author(s): Strzelczyk, P., Bujacz, A., Bujacz, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Ferrocene-Biotin Conjugates Targeting Cancer Cells: Synthesis, Interaction with Avidin, Cytotoxic Properties and the Crystal Structure of the Complex of Avidin with a Biotin-Linker-Ferrocene Conjugate

Plazuk, D., Zakrzewski, J., Salmain, M., Blauz, A., Rychlik, B., Strzelczyk, P., Bujacz, A., Bujacz, G.

(2013) Organometallics 32: 5774-5783

• DOI: https://doi.org/10.1021/om4003126

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: 30.35 kDa 
• Atom Count: 2,175 
• Modeled Residue Count: 247 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avidin	A, B	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
B6F	C [auth A], E [auth B]	[(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{6-[(6-{[5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoyl]amino}hexanoyl)amino]hexanoyl}cyclopentadienyl]iron C32 H38 Fe N4 O4 S GEJZIMWXLQTIFK-WOZYLDAHSA-N
NAG	D [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.693	α = 90
b = 78.656	β = 90
c = 42.762	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Strzelczyk, P., Bujacz, A., Bujacz, G.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-06
  Changes: Structure summary