1ND0

CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction

Zhu, X., Heine, A., Monnat, F., Houk, K.N., Janda, K.D., Wilson, I.A.

(2003) J.Mol.Biol. 329: 69-83

  • Primary Citation of Related Structures:  
  • Also Cited By: 1RUM, 1RUP, 1RUL, 1RUA, 1RUK, 1RU9

  • PubMed Abstract: 

    • Antibody 4C6 efficiently catalyzes a cationic cyclization reaction. Crystal structures of the antibody 4C6 Fab in complex with benzoic acid and in complex with its eliciting hapten were determined to 1.30A and 2.45A resolution, respectively. These cr ...

    Antibody 4C6 efficiently catalyzes a cationic cyclization reaction. Crystal structures of the antibody 4C6 Fab in complex with benzoic acid and in complex with its eliciting hapten were determined to 1.30A and 2.45A resolution, respectively. These crystal structures, together with computational analysis, have elucidated a possible mechanism for the monocyclization reaction. The hapten complex revealed a combining site pocket with high shape complementarity to the hapten. This active site cleft is dominated by aromatic residues that shield the highly reactive carbocation intermediates from solvent and stabilize the carbocation intermediates through cation-pi interactions. Modeling of an acyclic olefinic sulfonate ester substrate and the transition state (TS) structures shows that the chair-like transition state is favored, and trapping by water directly produces trans-2-(dimethylphenylsilyl)-cyclohexanol, whereas the less favored boat-like transition state leads to cyclohexene. The only significant change observed upon hapten binding is a side-chain rotation of Trp(L89), which reorients to form the base of the combining site. Intriguingly, a benzoic acid molecule was sequestered in the combining site of the unliganded antibody. The 4C6 active site was compared to that observed in a previously reported tandem cyclization antibody 19A4 hapten complex. These cationic cyclization antibodies exhibit convergent structural features with terpenoid cyclases that appear to be important for catalysis.

    Organizational Affiliation: 

    Department of Molecular Biology BBC206, The 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 IGG2A
A, C, E, G
219Mus musculusMutation(s): 0 
Gene Names: Igk
Find proteins for Q58EU8 (Mus musculus)
Go to UniProtKB:  Q58EU8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN IGG2A
B, D, F, H
222Mus musculusMutation(s): 0 
Gene Names: Igh-1a
Find proteins for P01865 (Mus musculus)
Go to UniProtKB:  P01865
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
B, D, F, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DP4
Query on DP4
Download SDF File 
Download CCD File 
A, C, E, G
(1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide
C14 H23 N O Si
HDJXTRKZEHHECC-GASCZTMLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 36.572α = 75.51
b = 95.164β = 88.64
c = 141.058γ = 89.28
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2002-12-05 
  • Released Date: 2003-05-13 
  • Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History 

  • Version 1.0: 2003-05-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance