2JB6

Fab fragment in complex with small molecule hapten, crystal form-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fab Mor03268 Triggers Absorption Shift of a Diagnostic Dye Via Packaging in a Solvent-Shielded Fab Dimer Interface

Hillig, R.C.Urlinger, S.Fanghanel, J.Brocks, B.Haenel, C.Stark, Y.Sulzle, D.Svergun, D.I.Baesler, S.Malawski, G.Moosmayer, D.Menrad, A.Schirner, M.Licha, K.

(2008) J Mol Biol 377: 206

  • DOI: 10.1016/j.jmb.2007.12.071
  • Primary Citation of Related Structures:  
    2JB6, 2JB5

  • PubMed Abstract: 
  • Molecular interactions between near-IR fluorescent probes and specific antibodies may be exploited to generate novel smart probes for diagnostic imaging. Using a new phage display technology, we developed such antibody Fab fragments with subnanomolar ...

    Molecular interactions between near-IR fluorescent probes and specific antibodies may be exploited to generate novel smart probes for diagnostic imaging. Using a new phage display technology, we developed such antibody Fab fragments with subnanomolar binding affinity for tetrasulfocyanine, a near-IR in vivo imaging agent. Unexpectedly, some Fabs induced redshifts of the dye absorption peak of up to 44 nm. This is the largest shift reported for a biological system so far. Crystal structure determination and absorption spectroscopy in the crystal in combination with microcalorimetry and small-angle X-ray scattering in solution revealed that the redshift is triggered by formation of a Fab dimer, with tetrasulfocyanine being buried in a fully closed protein cavity within the dimer interface. The derived principle of shifting the absorption peak of a symmetric dye via packaging within a Fab dimer interface may be transferred to other diagnostic fluorophores, opening the way towards smart imaging probes that change their wavelength upon interaction with an antibody.


    Related Citations: 
    • Crystallization and Molecular-Replacement Solution of a Diagnostic Fluorescent Dye in Complex with a Specific Fab Fragment.
      Hillig, R.C., Baesler, S., Urlinger, S., Stark, Y., Bauer, S., Badock, V., Huber, M., Bahr, I., Schirner, M., Licha, K.
      (2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 217

    Organizational Affiliation

    Bayer Schering Pharma AG, Global Drug Discovery, 13342 Berlin, Germany. roman.hillig@bayerhealthcare.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAB FRAGMENT MOR03268 LIGHT CHAINAL216Homo sapiensMutation(s): 0 
Gene Names: IGLC2
Find proteins for P0DOY2 (Homo sapiens)
Explore P0DOY2 
Go to UniProtKB:  P0DOY2
NIH Common Fund Data Resources
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FAB FRAGMENT MOR03268 HEAVY CHAINBH244Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T5C
Query on T5C

Download CCD File 
B, H
2-{(1E,3Z,5E,7E)-7-[3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]-4-METHYLHEPTA-1,3,5-TRIEN-1-YL}-3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-3H-INDOLIUM
C32 H39 N2 O12 S4
WKWHOLCUESSZIQ-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TSCKd :  0.01100000087171793   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.028α = 90
b = 77.028β = 90
c = 379.128γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance