Crystal structure of cortisol complexed with its nanobody at pH 3.5

Experimental Data Snapshot

  • Resolution: 1.57 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Structural insights into the mechanism of single domain VHH antibody binding to cortisol.

Ding, L.Wang, Z.Zhong, P.Jiang, H.Zhao, Z.Zhang, Y.Ren, Z.Ding, Y.

(2019) FEBS Lett 593: 1248-1256

  • DOI: https://doi.org/10.1002/1873-3468.13398
  • Primary Citation of Related Structures:  
    6ITP, 6ITQ

  • PubMed Abstract: 

    To date, few structural models of VHH antibody binding to low molecular weight haptens have been reported. Here, we report the crystal structure of cortisol binding to its VHH antibody NbCor at pH 3.5 and 10.5. Cortisol binds to NbCor mainly by burying itself under the tunnel formed by the complementarity determining region 1 (CDR1) of NbCor. The affinity of NbCor binding to cortisol and similar compounds was also verified by a microscale thermophoresis assay. Combining our findings with several previously reported structures of hapten-VHH antibody complexes, we propose that VHH antibodies exhibit a special mechanism of binding small haptens by encapsulating them in a tunnel formed by CDR1. Our findings provide useful structural information for the further development and optimization of hapten-specific VHH antibodies.

  • Organizational Affiliation

    Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-cortisol camelid antibody
A, B
127Camelus bactrianusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HCY (Subject of Investigation/LOI)
Query on HCY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C21 H30 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 1.57 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.043α = 90
b = 95.043β = 90
c = 95.043γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)China31470764
National Science Foundation (China)China91527305

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description