5VL2

The hapten triclocarban bound to the single domain camelid nanobody VHH T4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and specificity of several triclocarban-binding single domain camelid antibody fragments.

Tabares-da Rosa, S.Wogulis, L.A.Wogulis, M.D.Gonzalez-Sapienza, G.Wilson, D.K.

(2019) J. Mol. Recognit. 32: e2755-e2755

  • DOI: 10.1002/jmr.2755
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The variable VHH domains of camelid single chain antibodies have been useful in numerous biotechnology applications due to their simplicity, biophysical properties, and abilities to bind to their cognate antigens with high affinities and specificity. ...

    The variable VHH domains of camelid single chain antibodies have been useful in numerous biotechnology applications due to their simplicity, biophysical properties, and abilities to bind to their cognate antigens with high affinities and specificity. Their interactions with proteins have been well-studied, but considerably less work has been done to characterize their ability to bind haptens. A high-resolution structural study of three nanobodies (T4, T9, and T10) which have been shown to bind triclocarban (TCC, 3-(4-chlorophenyl)-1-(3,4-dichlorophenyl)urea) with near-nanomolar affinity shows that binding occurs in a tunnel largely formed by CDR1 rather than a surface or lateral binding mode seen in other nanobody-hapten interactions. Additional significant interactions are formed with a non-hypervariable loop, sometimes dubbed "CDR4". A comparison of apo and holo forms of T9 and T10 shows that the binding site undergoes little conformational change upon binding of TCC. Structures of three nanobody-TCC complexes demonstrated there was not a standard binding mode. T4 and T9 have a high degree of sequence identity and bind the hapten in a nearly identical manner, while the more divergent T10 binds TCC in a slightly displaced orientation with the urea moiety rotated approximately 180° along the long axis of the molecule. In addition to methotrexate, this is the second report of haptens binding in a tunnel formed by CDR1, suggesting that compounds with similar hydrophobicity and shape could be recognized by nanobodies in analogous fashion. Structure-guided mutations failed to improve binding affinity for T4 and T9 underscoring the high degree of natural optimization.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.,Cátedra de Inmunología, Facultad de Química, Instituto de Higiene, UDELAR, Uruguay.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T4 nanobody
A, B, C, D, E, F, G, H
132N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9EG
Query on 9EG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
N-(4-chlorophenyl)-N'-(3,4-dichlorophenyl)urea
C13 H9 Cl3 N2 O
ICUTUKXCWQYESQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9EGIC50: 20 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 98.803α = 90.00
b = 55.304β = 111.66
c = 103.426γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references
  • Version 1.2: 2018-12-26
    Type: Data collection, Database references