3T65

S25-2- A(2-8)KDO disaccharide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Germline antibody recognition of distinct carbohydrate epitopes.

Nguyen, H.P.Seto, N.O.MacKenzie, C.R.Brade, L.Kosma, P.Brade, H.Evans, S.V.

(2003) Nat.Struct.Mol.Biol. 10: 1019-1025

  • DOI: 10.1038/nsb1014
  • Primary Citation of Related Structures:  1Q9K, 1Q9L, 1Q9O, 1Q9Q, 1Q9R, 1Q9T, 1Q9V, 1Q9W, 3SY0, 3T4Y, 3T77

  • PubMed Abstract: 
  • High-resolution structures reveal how a germline antibody can recognize a range of clinically relevant carbohydrate epitopes. The germline response to a carbohydrate immunogen can be critical to survivability, with selection for antibody gene segment ...

    High-resolution structures reveal how a germline antibody can recognize a range of clinically relevant carbohydrate epitopes. The germline response to a carbohydrate immunogen can be critical to survivability, with selection for antibody gene segments that both confer protection against common pathogens and retain the flexibility to adapt to new disease organisms. We show here that antibody S25-2 binds several distinct inner-core epitopes of bacterial lipopolysaccharides (LPSs) by linking an inherited monosaccharide residue binding site with a subset of complementarity-determining regions (CDRs) of limited flexibility positioned to recognize the remainder of an array of different epitopes. This strategy allows germline antibodies to adapt to different epitopes while minimizing entropic penalties associated with the immobilization of labile CDRs upon binding of antigen, and provides insight into the link between the genetic origin of individual CDRs and their respective roles in antigen recognition.


    Organizational Affiliation

    Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S25-2 FAB (IGG1K) heavy chain
B
222N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
S25-2 FAB (IGG1K) light chain
A
219N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
KDA
Query on KDA

Download SDF File 
Download CCD File 
B
(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
C11 H18 O8
LEEKAQBTVJRLOA-UEWQFTGXSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
KDO
Query on KDO

Download SDF File 
Download CCD File 
B
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.900α = 90.00
b = 81.600β = 90.00
c = 131.500γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release