2GH7

Epi-biotin complex with core streptavidin


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 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 ...

    (+)-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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
StreptavidinA, B127Streptomyces avidiniiMutation(s): 0 
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTNΔH:  66.94000244140625   kJ/mol  BindingDB
BTNΔH:  123.01000213623047   kJ/mol  BindingDB
BTNKd:  1   nM  BindingDB
BTNΔH:  117.98999786376953   kJ/mol  BindingDB
BTNΔH:  104.18000030517578   kJ/mol  BindingDB
BTNΔH:  115.05999755859375   kJ/mol  BindingDB
BTNΔH:  97.48999786376953   kJ/mol  BindingDB
BTNΔH:  100.41999816894531   kJ/mol  BindingDB
BTNΔH:  75.30999755859375   kJ/mol  BindingDB
BTNKd:  0.00010000000474974513   nM  Binding MOAD
BTQKd:  0.00010000000474974513   nM  Binding MOAD
BTNΔH:  102.51000213623047   kJ/mol  BindingDB
BTNKd :  0.00010000000474974513   nM  PDBBind
BTNΔH:  89.95999908447266   kJ/mol  BindingDB
BTNΔH:  107.52999877929688   kJ/mol  BindingDB
BTNΔH:  90.37000274658203   kJ/mol  BindingDB
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 = 46.39α = 90
b = 93.811β = 90
c = 104.449γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
HKL-2000data scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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