1A4K

DIELS ALDER CATALYTIC ANTIBODY WITH TRANSITION STATE ANALOGUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Immunological origins of binding and catalysis in a Diels-Alderase antibody.

Romesberg, F.E.Spiller, B.Schultz, P.G.Stevens, R.C.

(1998) Science 279: 1929-1933

  • Primary Citation of Related Structures:  1A4J

  • PubMed Abstract: 
  • The three-dimensional structure of an antibody (39-A11) that catalyzes a Diels-Alder reaction has been determined. The structure suggests that the antibody catalyzes this pericyclic reaction through a combination of packing and hydrogen-bonding inter ...

    The three-dimensional structure of an antibody (39-A11) that catalyzes a Diels-Alder reaction has been determined. The structure suggests that the antibody catalyzes this pericyclic reaction through a combination of packing and hydrogen-bonding interactions that control the relative geometries of the bound substrates and electronic distribution in the dienophile. A single somatic mutation, serine-91 of the light chain to valine, is largely responsible for the increase in affinity and catalytic activity of the affinity-matured antibody. Structural and functional studies of the germ-line precursor suggest that 39-A11 and related antibodies derive from a family of germ-line genes that have been selected throughout evolution for the ability of the encoded proteins to form a polyspecific combining site. Germ line-encoded antibodies of this type, which can rapidly evolve into high-affinity receptors for a broad range of structures, may help to expand the binding potential associated with the structural diversity of the primary antibody repertoire.


    Organizational Affiliation

    Howard Hughes Medical Institute and the Department of Chemistry, University of California, Berkeley, CA 94720, USA. 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY FAB
L, A
217Homo sapiensGene Names: IGKC
Find proteins for P01834 (Homo sapiens)
Go to UniProtKB:  P01834
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY FAB
H, B
219N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FRA
Query on FRA

Download SDF File 
Download CCD File 
B, H
[4-(4-ACETYLAMINO-PHENYL)-3,5-DIOXO-4-AZA-TRICYCLO[5.2.2.0 2,6]UNDEC-1-YLCARBAMOYLOXY]-ACETIC ACID
C21 H23 N3 O7
WBCOLMYVEBTZOA-OKRSVSQCSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, L
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FRAKd: 10 nM BINDINGMOAD
FRAKd: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.316α = 90.00
b = 96.823β = 90.00
c = 172.730γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-13
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance