3KDM

Crystal Structure of Human Anti-steroid Fab 5F2 in Complex with Testosterone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The testosterone binding mechanism of an antibody derived from a naive human scFv library

Niemi, M.H.Takkinen, K.Amundsen, L.K.Soderlund, H.Rouvinen, J.Hoyhtya, M.

(2010) J.Mol.Recognit. 24: 209-219

  • DOI: 10.1002/jmr.1039

  • PubMed Abstract: 
  • A testosterone binding scFv antibody was isolated from a naïve human library with a modest size of 10(8) clones. The crystal structure of the Fab fragment form of the 5F2 antibody clone complexed with testosterone determined at 1.5 Å resolution shows ...

    A testosterone binding scFv antibody was isolated from a naïve human library with a modest size of 10(8) clones. The crystal structure of the Fab fragment form of the 5F2 antibody clone complexed with testosterone determined at 1.5 Å resolution shows that the hapten is bound deeply in the antibody binding pocket. In addition to the interactions with framework residues only CDR-L3 and CDR-H3 loops interact with testosterone and the heavy chain forms the majority of the contacts with the hapten. The testosterone binding site of the 5F2 antibody with a high abundance of aromatic amino acid residues shows similarity with an in vitro affinity matured antibody having around 300 times higher affinity. The moderate affinity of the 5F2 antibody originates from the different orientation of the hapten and few light chain contacts. This is the first three-dimensional structure of a human steroid hormone binding antibody that has been isolated from a naïve human repertoire.


    Organizational Affiliation

    Department of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin light chain
L, A
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin heavy chain
H, B
225N/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
TES
Query on TES

Download SDF File 
Download CCD File 
B, H
TESTOSTERONE
C19 H28 O2
MUMGGOZAMZWBJJ-DYKIIFRCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
B, H
L-PEPTIDE LINKINGC5 H7 N O3GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TESKd: 100 nM BINDINGMOAD
TESKd: 100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 66.750α = 81.32
b = 67.080β = 69.30
c = 67.060γ = 69.27
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-12-07
    Type: Database references