1KNO

CRYSTAL STRUCTURE OF THE COMPLEX OF A CATALYTIC ANTIBODY FAB WITH A TRANSITION STATE ANALOG: STRUCTURAL SIMILARITIES IN ESTERASE-LIKE ABZYMES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies.

Charbonnier, J.B.Carpenter, E.Gigant, B.Golinelli-Pimpaneau, B.Eshhar, Z.Green, B.S.Knossow, M.

(1995) Proc Natl Acad Sci U S A 92: 11721-11725

  • DOI: 10.1073/pnas.92.25.11721
  • Primary Citation of Related Structures:  
    1KNO

  • PubMed Abstract: 
  • The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and subst ...

    The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and substrate specificity. Comparison of this structure with that of the uncomplexed Fab fragment suggests hapten-induced conformational changes: the shape of the combining site changes from a shallow groove in the uncomplexed Fab to a deep pocket where the hapten is buried. Three hydrogen-bond donors appear to stabilize the charged phosphonate group of the hapten: two NH groups of the heavy (H) chain complementarity-determining region 3 (H3 CDR) polypeptide chain and the side-chain of histidine-H35 in the H chain (His-H35) in the H1 CDR. The combining site shows striking structural similarities to that of antibody 17E8, which also has esterase activity. Both catalytic antibody ("abzyme") structures suggest that oxyanion stabilization plays a significant role in their rate acceleration. Additional catalytic groups that improve efficiency are not necessarily induced by the eliciting hapten; these groups may occur because of the variability in the combining sites of different monoclonal antibodies that bind to the same hapten.


    Related Citations: 
    • Differences in the Biochemical Properties of Esterolytic Antibodies Correlate with Structural Diversity
      Zemel, R., Schindler, D.G., Tawfik, D.S., Eshhar, Z., Green, B.S.
      (1994) Mol Immunol 31: 127
    • Crystal Structure of a Catalytic Antibody Fab with Esterase-Like Activity
      Golinelli-Pimpaneau, B., Gigant, B., Bizebard, T., Navaza, J., Saludjian, P., Zemel, R., Tawfik, D.S., Eshhar, Z., Green, B.S., Knossow, M.
      (1994) Structure 2: 175

    Organizational Affiliation

    Laboratoire de Biologie Structurale, Centre National de la Recherche Scientifique, Université Paris Sud, Gif-sur-Yvette, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A FAB FRAGMENT CNJ206ACE214Mus musculusMutation(s): 0 
Gene Names: Igkc
Find proteins for P01837 (Mus musculus)
Explore P01837 
Go to UniProtKB:  P01837
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A FAB FRAGMENT CNJ206BDF220Mus musculusMutation(s): 0 
Gene Names: Ighg
Find proteins for P01863 (Mus musculus)
Explore P01863 
Go to UniProtKB:  P01863
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNP
Query on PNP

Download CCD File 
B, D, F
METHYL-PHOSPHONIC ACID MONO-(4-NITRO-PHENYL) ESTER
C7 H8 N O5 P
VJPXTXIEAOSJBR-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.1α = 93.8
b = 76.9β = 93.9
c = 88.3γ = 115.6
Software Package:
Software NamePurpose
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance