2GH7

Epi-biotin complex with core streptavidin

• PDB DOI: https://doi.org/10.2210/pdb2GH7/pdb

• Classification: BIOTIN BINDING PROTEIN
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-26 Released: 2006-04-18 
• Deposition Author(s): Le Trong, I., Aubert, D.G.L., Thomas, N.R., Stenkamp, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.152 
• R-Value Observed: 0.141 

Literature

The high-resolution structure of (+)-epi-biotin bound to streptavidin.

Le Trong, I., Aubert, D.G., Thomas, N.R., Stenkamp, R.E.

(2006) Acta Crystallogr D Biol Crystallogr 62: 576-581

• PubMed: 16699183 
• DOI: https://doi.org/10.1107/S0907444906011887
• Primary Citation of Related Structures:  
  2F01, 2GH7


• PubMed Abstract: 
  

  (+)-Epi-biotin differs from (+)-biotin in the configuration of the chiral center at atom C2. This could lead to a difference in the mode of binding of (+)-epi-biotin to streptavidin, a natural protein receptor for (+)-biotin. Diffraction data were collected to a maximum of 0.85 Angstrom resolution for structural analysis of the complex of streptavidin with a sample of (+)-epi-biotin and refinement was carried out at both 1.0 and 0.85 Angstrom resolution. The structure determination shows a superposition of two ligands in the binding site, (+)-biotin and (+)-epi-biotin. The molecules overlap in the model for the complex except for the position of S1 in the tetrahydrothiophene ring. Differences in the conformation of the ring permits binding of each molecule to streptavidin with little observable difference in the protein structures at this high resolution.

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Organizational Affiliation: 

Departments of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.82 kDa 
• Atom Count: 2,209 
• Modelled Residue Count: 241 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTQ	D [auth A], H [auth B]	EPI-BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-OOZYFLPDSA-N
BTN	C [auth A], G [auth B]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N
GOL	E [auth A], F [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BTN	BindingDB:  2GH7	Kd: 0 (nM) from 1 assay(s)
		ΔH: min: -1.23e+2, max: -6.69e+1 (kJ/mol) from 12 assay(s)
	PDBBind:  2GH7	Kd: 1.00e-4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.152 
• R-Value Observed: 0.141 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.39	α = 90
b = 93.811	β = 90
c = 104.449	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Le Trong, I., Aubert, D.G.L., Thomas, N.R., Stenkamp, R.E.

Revision History  

• Version 1.0: 2006-04-18
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations