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 
  • R-Value Observed: 0.184 

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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

  • DOI: 10.1126/science.279.5358.1934
  • Primary Citation of Related Structures:  
    1A3L

  • 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 counterpart and that yields a single regioisomer in high enantiomeric excess ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN FAB 13G5 (LIGHT CHAIN)A [auth L]217Mus musculusMutation(s): 0 
Gene Names: Igkc
UniProt
Find proteins for P01837 (Mus musculus)
Explore P01837 
Go to UniProtKB:  P01837
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN FAB 13G5 (HEAVY CHAIN)B [auth H]218Mus musculusMutation(s): 0 
Gene Names: Ighg1Igh-4
UniProt
Find proteins for P01869 (Mus musculus)
Explore P01869 
Go to UniProtKB:  P01869
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CFC (Subject of Investigation/LOI)
Query on CFC

Download Ideal Coordinates CCD File 
C [auth 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 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.9α = 90
b = 40.5β = 109
c = 67.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96model building
SHELXL-96refinement
SHELXL-96phasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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