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: 3.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 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.USA 92: 11721-11725


  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A FAB FRAGMENT CNJ206
A, C, E
214Mus musculusMutation(s): 0 
Gene Names: Igkc
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A FAB FRAGMENT CNJ206
B, D, F
220Mus musculusMutation(s): 0 
Gene Names: Ighg
Find proteins for P01863 (Mus musculus)
Go to UniProtKB:  P01863
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PNP
Query on PNP

Download SDF File 
Download CCD File 
B, D, F
METHYL-PHOSPHONIC ACID MONO-(4-NITRO-PHENYL) ESTER
4-NITROPHENYL HYDROGEN METHYLPHOSPHONATE
C7 H8 N O5 P
VJPXTXIEAOSJBR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.200 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 74.100α = 93.80
b = 76.900β = 93.90
c = 88.300γ = 115.60
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
MOSFLMdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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