3VGW

Crystal structure of monoAc-biotin-avidin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Rational development of caged-biotin protein-labeling agents and some applications in live cells

Terai, T.Maki, E.Sugiyama, S.Takahashi, Y.Matsumura, H.Mori, Y.Nagano, T.

(2011) Chem Biol 18: 1261-1272

  • DOI: https://doi.org/10.1016/j.chembiol.2011.09.007
  • Primary Citation of Related Structures:  
    3VGW, 3VHH, 3VHI, 3VHM

  • PubMed Abstract: 

    Biotin-(strept)avidin complex is widely used in biotechnology because of its extremely high binding constant, but there is no report describing spatiotemporally controlled formation of the complex in live cells. Here, based on X-ray crystal structure analysis and calorimetric data, we designed and synthesized photoreleasable biotins, which show greatly reduced affinity for (strept)avidin, but recover native affinity after UV irradiation. For application at the cell surface, we introduced an amine-reactive moiety into these "caged" biotin molecules. Specific fluorescence imaging of live cells that had been labeled with these agents and then UV-irradiated, was accomplished by addition of streptavidin conjugated with a fluorophore. We also demonstrated the applicability of these compounds for UV-irradiated-cell-specific drug delivery by using caged-biotin-labeled cells, a prodrug, and streptavidin conjugated with a prodrug-activating enzyme.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Avidin
A, B, C, D, E
A, B, C, D, E, F, G, H
123Gallus gallusMutation(s): 0 
UniProt
Find proteins for P02701 (Gallus gallus)
Explore P02701 
Go to UniProtKB:  P02701
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02701
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NVZ
Query on NVZ

Download Ideal Coordinates CCD File 
AA [auth F]
DA [auth G]
HA [auth H]
I [auth A]
M [auth B]
AA [auth F],
DA [auth G],
HA [auth H],
I [auth A],
M [auth B],
P [auth C],
T [auth D],
W [auth E]
5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
C12 H18 N2 O4 S
LXKFOEIWWHPOIN-QXEWZRGKSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth G]
IA [auth H]
J [auth A]
N [auth B]
BA [auth F],
EA [auth G],
IA [auth H],
J [auth A],
N [auth B],
Q [auth C],
U [auth D],
X [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth F]
FA [auth G]
GA [auth G]
JA [auth H]
K [auth A]
CA [auth F],
FA [auth G],
GA [auth G],
JA [auth H],
K [auth A],
L [auth A],
O [auth B],
R [auth C],
S [auth C],
V [auth D],
Y [auth E],
Z [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
NVZ Binding MOAD:  3VGW Ka: 2.00e+5 (M^-1) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.01α = 90
b = 81.224β = 92.47
c = 74.41γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary