1YNK

Identification of Key residues of the NC6.8 Fab antibody fragment binding to synthetic sweeteners: Crystal structure of NC6.8 co-crystalized with high potency sweetener compound SC45647


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cocrystal Structures of NC6.8 Fab Identify Key Interactions for High Potency Sweetener Recognition: Implications for the Design of Synthetic Sweeteners

Gokulan, K.Khare, S.Ronning, D.R.Linthicum, S.D.Sacchettini, J.C.Rupp, B.

(2005) Biochemistry 44: 9889-9898

  • DOI: 10.1021/bi050613u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of the murine monoclonal IgG2b(kappa) antibody NC6.8 Fab fragment complexed with high-potency sweetener compound SC45647 and nontasting high-affinity antagonist TES have been determined. The crystal structures show how sweetene ...

    The crystal structures of the murine monoclonal IgG2b(kappa) antibody NC6.8 Fab fragment complexed with high-potency sweetener compound SC45647 and nontasting high-affinity antagonist TES have been determined. The crystal structures show how sweetener potency is fine-tuned by multiple interactions between specific receptor residues and the functionally different groups of the sweeteners. Comparative analysis with the structure of NC6.8 complexed with the super-potency sweetener NC174 reveals that although the same residues in the antigen binding pocket of NC6.8 interact with the zwitterionic, trisubstituted guanidinium sweeteners as well as TES, specific differences exist and provide guidance for the design of new artificial sweeteners. In case of the nonsweetener TES, the interactions with the receptor are indirectly mediated through a hydrogen bonded water network, while the sweeteners bind with high affinity directly to the receptor. The presence of a hydrophobic group interacting with multiple receptor residues as a major determinant for sweet taste has been confirmed. The nature of the hydrophobic group is likely a discriminator for super- versus high-potency sweeteners, which can be exploited in the design of new, highly potent sweetener compounds. Overall similarities and partial conservation of interactions indicate that the NC6.8 Fab surrogate is representing crucial features of the T1R2 taste receptor VFTM binding site.


    Organizational Affiliation

    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
immunoglobulin kappa light chain
L
219Mus musculusMutation(s): 0 
Gene Names: Igkc (Igk-C)
Find proteins for A2P1G9 (Mus musculus)
Go to UniProtKB:  A2P1G9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ig gamma heavy chain
H
219Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q6PJB2 (Mus musculus)
Go to UniProtKB:  Q6PJB2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SC5
Query on SC5

Download SDF File 
Download CCD File 
H
2-[((R)-{[4-(AMINOMETHYL)PHENYL]AMINO}{[(1R)-1-PHENYLETHYL]AMINO}METHYL)AMINO]ETHANE-1,1-DIOL
SC45647
C18 H26 N4 O2
LPSXGZAUAOMRNU-FZKQIMNGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.600α = 90.00
b = 48.190β = 109.04
c = 75.350γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
shakemodel building
REFMACrefinement
ARP/wARPmodel building
SnBphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description