1YEG

STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structures of a hydrolytic antibody and of complexes elucidate catalytic pathway from substrate binding and transition state stabilization through water attack and product release.

Gigant, B.Charbonnier, J.B.Eshhar, Z.Green, B.S.Knossow, M.

(1997) Proc.Natl.Acad.Sci.USA 94: 7857-7861

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The x-ray structures of the unliganded esterase-like catalytic antibody D2.3 and its complexes with a substrate analogue and with one of the reaction products are analyzed. Together with the structure of the phosphonate transition state analogue hapt ...

    The x-ray structures of the unliganded esterase-like catalytic antibody D2.3 and its complexes with a substrate analogue and with one of the reaction products are analyzed. Together with the structure of the phosphonate transition state analogue hapten complex, these crystal structures provide a complete description of the reaction pathway. At alkaline pH, D2.3 acts by preferential stabilization of the negatively charged oxyanion intermediate of the reaction that results from hydroxide attack on the substrate. A tyrosine residue plays a crucial role in catalysis: it activates the ester substrate and, together with an asparagine, it stabilizes the oxyanion intermediate. A canal allows facile diffusion of water molecules to the reaction center that is deeply buried in the structure. Residues bordering this canal provide targets for mutagenesis to introduce a general base in the vicinity of the reaction center.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Unité Propre de Recherche 9063 Centre National de la Recherche Scientifique, Bat. 34, Avenue de la Terrasse, 91198 Gif sur Yvette Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A FAB FRAGMENT
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A FAB FRAGMENT
H
222Mus musculusMutation(s): 0 
Gene Names: Ighg
Find proteins for P01863 (Mus musculus)
Go to UniProtKB:  P01863
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
H
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
BPN
Query on BPN

Download SDF File 
Download CCD File 
L
PARANITROBENZYL ALCOHOL
C7 H7 N O3
JKTYGPATCNUWKN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.550α = 90.00
b = 78.550β = 90.00
c = 159.500γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
X-PLORphasing
AGROVATAdata reduction
X-PLORrefinement
AGROVATAdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-03
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance