1I3U

THREE-DIMENSIONAL STRUCTURE OF A LLAMA VHH DOMAIN COMPLEXED WITH THE DYE RR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lateral recognition of a dye hapten by a llama VHH domain.

Spinelli, S.Tegoni, M.Frenken, L.van Vliet, C.Cambillau, C.

(2001) J.Mol.Biol. 311: 123-129

  • DOI: 10.1006/jmbi.2001.4856
  • Primary Citation of Related Structures:  1I3V

  • PubMed Abstract: 
  • Camelids, camels and llamas, have a unique immune system able to produce heavy-chain only antibodies. Their VH domains (VHHs) are the smallest binding units produced by immune systems, and therefore suitable for biotechnological applications through ...

    Camelids, camels and llamas, have a unique immune system able to produce heavy-chain only antibodies. Their VH domains (VHHs) are the smallest binding units produced by immune systems, and therefore suitable for biotechnological applications through heterologous expression. The recognition of protein antigens by these VHHs is rather well documented, while less is known about the VHH/hapten interactions. The recently reported X-ray structure of a VHH in complex with a copper-containing azo-dye settled the ability of VHH to recognize haptens by forming a cavity between the three complementarity-determining regions (CDR). Here we report the structures of a VHH (VHH A52) free or complexed with an azo-dye, RR1, without metal ion. The structure of the complex illustrates the involvement of CDR2, CDR3 and a framework residue in a lateral interaction with the hapten. Such a lateral combining site is comparable to that found in classical antibodies, although in the absence of the VL.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I and II, 31 Chemin Joseph Aiguier, Marseille Cedex 20, UMR-6098, 13402, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY VHH LAMA DOMAIN
A
127N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RR1
Query on RR1

Download SDF File 
Download CCD File 
A
5-(4,6-DIAMINO-[1,3,5]TRIAZIN-2-YLAMINO)-4-HYDROXY-3-(2-SULFO-PHENYLAZO)-NAPHTHALENE-2,7-DISULFONIC ACID
REACTIVE RED 1 DYE
C19 H16 N8 O10 S3
LOCFSBZWHQIILX-CYYJNZCTSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGN
Query on CGN
A
NON-POLYMERC5 H7 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.232 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 77.435α = 90.00
b = 77.435β = 90.00
c = 175.019γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance