9PUB | pdb_00009pub

Biotin-streptavidin binding

• PDB DOI: https://doi.org/10.2210/pdb9PUB/pdb

• Classification: PROTEIN BINDING
• Organism(s): Streptomyces avidinii
• Mutation(s): No 


• Deposited: 2025-07-30 Released: 2025-09-03 
• Deposition Author(s): Whitby, F.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.145 (Depositor), 0.146 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.132 (DCC) 

Starting Model: experimental

Literature

Streptavidin Structures

Giesler, R., Kay, M.S.

To be published.

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: 27.14 kDa 
• Atom Count: 2,418 
• Modeled Residue Count: 243 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A [auth J], B [auth K]	127	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTN (Subject of Investigation/LOI)	C [auth J], D [auth K]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N
GOL	E [auth K]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.145 (Depositor), 0.146 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.132 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.688	α = 90
b = 94.415	β = 90
c = 105.14	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Whitby, F.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54 AI170856

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release