1SRI | pdb_00001sri

STRUCTURE-BASED DESIGN OF SYNTHETIC AZOBENZENE LIGANDS FOR STREPTAVIDIN

• PDB DOI: https://doi.org/10.2210/pdb1SRI/pdb

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


• Deposited: 1994-02-17 Released: 1994-11-01 
• Deposition Author(s): Weber, P.C., Salemme, F.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Structure-Based Design of Synthetic Azobenzene Ligands for Streptavidin

Weber, P.C., Pantoliano, M.W., Simons, D.M., Salemme, F.R.

(1994) J Am Chem Soc 116: 2717

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)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 26.02 kDa 
• Atom Count: 1,958 
• Modeled Residue Count: 239 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STREPTAVIDIN	A, B	121	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMB	C [auth A], D [auth B]	2-((3',5'-DIMETHYL-4'-HYDROXYPHENYL)AZO)BENZOIC ACID C15 H14 N2 O3 ZMDQWZFZPGJFPM-WUKNDPDISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Observed: 0.175 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.6	α = 90
b = 106	β = 90
c = 47.9	γ = 90

Software Package:

Software Name	Purpose
PROFFT	refinement
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-11-01 
Deposition Author(s): Weber, P.C., Salemme, F.R.

Revision History  

• Version 1.0: 1994-11-01
  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 1.3: 2012-10-10
  Changes: Other
• Version 1.4: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.5: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary