2GH7

Epi-biotin complex with core streptavidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.152 

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.,Sect.D 62: 576-581

  • DOI: 10.1107/S0907444906011887
  • Primary Citation of Related Structures:  

  • 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 co ...

    (+)-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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Streptavidin
A, B
127Streptomyces avidiniiMutation(s): 0 
Find proteins for P22629 (Streptomyces avidinii)
Go to UniProtKB:  P22629
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTQ
Query on BTQ

Download SDF File 
Download CCD File 
A, B
EPI-BIOTIN
5-[(3AS,4R,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC ACID
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-OOZYFLPDSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BTN
Query on BTN

Download SDF File 
Download CCD File 
A, B
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.152 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 46.390α = 90.00
b = 93.811β = 90.00
c = 104.449γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance