1KEL

CATALYTIC ANTIBODY 28B4 FAB FRAGMENT COMPLEXED WITH HAPTEN (1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO] METHYLPHOSPHONIC ACID)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution.

Hsieh-Wilson, L.C.Schultz, P.G.Stevens, R.C.

(1996) Proc Natl Acad Sci U S A 93: 5363-5367

  • DOI: https://doi.org/10.1073/pnas.93.11.5363
  • Primary Citation of Related Structures:  
    1KEL, 1KEM

  • PubMed Abstract: 

    The x-ray crystal structures of the sulfide oxidase antibody 28B4 and of antibody 28B4 complexed with hapten have been solved at 2.2-angstrom and 1.9-angstrom resolution, respectively. To our knowledge, these structures are the highest resolution catalytic antibody structures to date and provide insight into the molecular mechanism of this antibody-catalyzed monooxygenation reaction. Specifically, the data suggest that entropic restriction plays a fundamental role in catalysis through the precise alignment of the thioether substrate and oxidant. The antibody active site also stabilizes developing charge on both sulfur and periodate in the transition state via cation-pi and electrostatic interactions, respectively. In addition to demonstrating that the active site of antibody 28B4 does indeed reflect the mechanistic information programmed in the aminophosphonic acid hapten, these high-resolution structures provide a basis for enhancing turnover rates through mutagenesis and improved hapten design.


  • Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, 94720, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
28B4 FABA [auth L]217Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
28B4 FABB [auth H]218Mus musculusMutation(s): 0 
UniProt
Find proteins for P01868 (Mus musculus)
Explore P01868 
Go to UniProtKB:  P01868
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01868
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AAH
Query on AAH

Download Ideal Coordinates CCD File 
C [auth H]1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO]METHYLPHOSPHONIC ACID
C13 H19 N2 O7 P
RWVBLRUMXIXUAR-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AAH PDBBind:  1KEL Kd: 52 (nM) from 1 assay(s)
Binding MOAD:  1KEL Kd: 52 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.7α = 94.3
b = 58.2β = 113.8
c = 43.2γ = 78.9
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance