2C1P

Fab-fragment of enantioselective antibody complexed with finrozole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of an Enantioselective Fab-Fragment in Free and Complex Forms.

Parkkinen, T.Nevanen, T.K.Koivula, A.Rouvinen, J.

(2006) J.Mol.Biol. 357: 471

  • DOI: 10.1016/j.jmb.2005.12.045
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enantioselective antibodies can separate the enantiomers of a chiral compound in a highly specific manner. We have recently reported the cloning and applications of a recombinant Fab-fragment, ENA11His, in the enantioseparation of a drug candidate, f ...

    Enantioselective antibodies can separate the enantiomers of a chiral compound in a highly specific manner. We have recently reported the cloning and applications of a recombinant Fab-fragment, ENA11His, in the enantioseparation of a drug candidate, finrozole, which contains two chiral centers. Here, the crystal structures of this enantioselective antibody Fab-fragment are determined in the absence of the hapten at a resolution of 2.75 A, and in the presence of the hapten at 2.05 A resolution. The conformation of the protein was found to be similar in both free and complex forms. The hapten molecule was tightly bound in a deep cleft between the light and heavy chains of the Fab-fragment. The complex structure also allowed us to describe the molecular basis for enantioselectivity and to deduce the absolute configurations of all the four different stereoisomers (a-d) of finrozole. The ENA11His antibody fragment selectively binds the SR (a) enantiomer from the racemic mixture of a and d-enantiomers, thus allowing separation from the pharmacologically most active RS enantiomer (d). In particular, Asp95 and Asn35 of the H-chain in the ENA11 His antibody seem to provide this specificity through hydrogen bonding.


    Organizational Affiliation

    Department of Chemistry, University of Joensuu, PO Box 111, FIN-80101 Joensuu, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGK-C PROTEIN
A, L
218Mus musculusMutation(s): 0 
Gene Names: Igk
Find proteins for Q58EU8 (Mus musculus)
Go to UniProtKB:  Q58EU8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGH-4 PROTEIN
B, H
217N/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
FNZ
Query on FNZ

Download SDF File 
Download CCD File 
B, H
4-[(1S,2R)-3-(4-FLUOROPHENYL)-2-HYDROXY-1-(1H-1,2,4-TRIAZOL-1-YL)PROPYL]BENZONITRILE
C18 H15 F N4 O
SLJZVZKQYSKYNV-MSOLQXFVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FNZKd: 4000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.815α = 90.00
b = 87.419β = 90.00
c = 141.684γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-07-24
    Type: Data collection