1QD0

CAMELID HEAVY CHAIN VARIABLE DOMAINS PROVIDE EFFICIENT COMBINING SITES TO HAPTENS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Camelid heavy-chain variable domains provide efficient combining sites to haptens.

Spinelli, S.Frenken, L.G.Hermans, P.Verrips, T.Brown, K.Tegoni, M.Cambillau, C.

(2000) Biochemistry 39: 1217-1222

  • DOI: https://doi.org/10.1021/bi991830w
  • Primary Citation of Related Structures:  
    1QD0

  • PubMed Abstract: 

    Camelids can produce antibodies devoid of light chains and CH1 domains (Hamers-Casterman, C. et al. (1993) Nature 363, 446-448). Camelid heavy-chain variable domains (VHH) have high affinities for protein antigens and the structures of two of these complexes have been determined (Desmyter, A. et al. (1996) Nature Struc. Biol. 3, 803-811; Decanniere, K. et al. (1999) Structure 7, 361-370). However, the small size of these VHHs and their monomeric nature bring into question their capacity to bind haptens. Here, we have successfully raised llama antibodies against the hapten azo-dye Reactive Red (RR6) and determined the crystal structure of the complex between a dimer of this hapten and a VHH fragment. The surface of interaction between the VHH and the dimeric hapten is large, with an area of ca. 300 A(2); this correlates well with the low-dissociation constant of 22 nM measured for the monomer. The VHH fragment provides an efficient combining site to the RR6, using its three CDR loops. In particular, CDR1 provides a strong interaction to the hapten through two histidine residues bound to its copper atoms. VHH fragments might, therefore, prove to be valuable tools for selecting, removing, or capturing haptens. They are likely to play a role in biotechnology extending beyond protein recognition alone.


  • Organizational Affiliation

    Architecture et Fonction des Macromolecules Biologiques, CNRS, UPR-9039, 31 Chemiin Joseph Aiguier, 13402 Marseille Cedex 20, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VHH-R2 ANTI-RR6 ANTIBODY128Lama glamaMutation(s): 0 
UniProt
Find proteins for A2KD59 (Lama glama)
Explore A2KD59 
Go to UniProtKB:  A2KD59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2KD59
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RR6
Query on RR6

Download Ideal Coordinates CCD File 
D [auth A]3-HYDROXY-7-(4-{1-[2-HYDROXY-3-(2-HYDROXY-5-SULFO-PHENYLAZO)-BENZYL]-2-SULFO-ETHYLAMINO}-[1,2,5]TRIAZIN-2-YLAMINO)-2-(2-HYDROXY-5-SULFO-PHENYLAZO)-NAPTHALENE-1,8-DISULFONIC ACID
C35 H25 N9 O22 S6
PJONDRDKCIFXDA-CHQNLTHESA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.7α = 90
b = 46.7β = 90
c = 121.1γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
AUTOMARdata reduction
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2018-02-28
    Changes: Experimental preparation