1A3L

CATALYSIS OF A DISFAVORED REACTION: AN ANTIBODY EXO DIELS-ALDERASE-TSA-INHIBITOR COMPLEX AT 1.95 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An antibody exo Diels-Alderase inhibitor complex at 1.95 angstrom resolution.

Heine, A.Stura, E.A.Yli-Kauhaluoma, J.T.Gao, C.Deng, Q.Beno, B.R.Houk, K.N.Janda, K.D.Wilson, I.A.

(1998) Science 279: 1934-1940

  • Also Cited By: 1RUQ, 1RUR

  • PubMed Abstract: 
  • A highly specific Diels-Alder protein catalyst was made by manipulating the antibody repertoire of the immune system. The catalytic antibody 13G5 catalyzes a disfavored exo Diels-Alder transformation in a reaction for which there is no natural enzyme ...

    A highly specific Diels-Alder protein catalyst was made by manipulating the antibody repertoire of the immune system. The catalytic antibody 13G5 catalyzes a disfavored exo Diels-Alder transformation in a reaction for which there is no natural enzyme counterpart and that yields a single regioisomer in high enantiomeric excess. The crystal structure of the antibody Fab in complex with a ferrocenyl inhibitor containing the essential haptenic core that elicited 13G5 was determined at 1.95 angstrom resolution. Three key antibody residues appear to be responsible for the observed catalysis and product control. Tyrosine-L36 acts as a Lewis acid activating the dienophile for nucleophilic attack, and asparagine-L91 and aspartic acid-H50 form hydrogen bonds to the carboxylate side chain that substitutes for the carbamate diene substrate. This hydrogen-bonding scheme leads to rate acceleration and also pronounced stereoselectivity. Docking experiments with the four possible ortho transition states of the reaction explain the specific exo effect and suggest that the (3R,4R)-exo stereoisomer is the preferred product.


    Organizational Affiliation

    The Skaggs Institute of Chemical Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN FAB 13G5 (LIGHT CHAIN)
L
217Mus musculusN/A
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN FAB 13G5 (HEAVY CHAIN)
H
218Mus musculusGene Names: Ighg1 (Igh-4)
Find proteins for P01869 (Mus musculus)
Go to UniProtKB:  P01869
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CFC
Query on CFC

Download SDF File 
Download CCD File 
L
1-CARBOXY-1'-[(DIMETHYLAMINO)-CARBONYL]FERROCENE
C14 H15 Fe N O3
QUKRDAUIFVLNSE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.265 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 182.900α = 90.00
b = 40.500β = 109.00
c = 67.700γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXL-96model building
SHELXL-96phasing
SHELXL-96refinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance