1KN4

CATALYTIC ANTIBODY D2.3 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Remarkable remote chiral recognition in a reaction mediated by a catalytic antibody.

D'Souza, L.J.Gigant, B.Knossow, M.Green, B.S.

(2002) J.Am.Chem.Soc. 124: 2114-2115

  • Primary Citation of Related Structures:  1KN2

  • PubMed Abstract: 
  • The crystal structures of catalytic antibody D2.3 Fab with the two enantiomers, 7D and 7L, which represent transition state analogues for the hydrolysis of the corresponding esters, 6D and 6L, were determined to better understand remarkable reactivit ...

    The crystal structures of catalytic antibody D2.3 Fab with the two enantiomers, 7D and 7L, which represent transition state analogues for the hydrolysis of the corresponding esters, 6D and 6L, were determined to better understand remarkable reactivity differences: the L-ester displayed significantly tighter binding (K(M)) and increased catalytic activity (k(cat)) with D2.3, even though the chiral center is 7 bonds distant from the reaction center. Surprisingly, the electron densities of the liganded phosphonates, 7D and 7L, within the D2.3 binding/reaction site were essentially identical, highlighting the subtle influences of protein interactions on chemical behavior.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, The Hebrew University, School of Pharmacy, P.O. Box 12065, Jerusalem 91120, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IG ANTIBODY D2.3 (LIGHT CHAIN)
L
219Mus musculusGene Names: Igk
Find proteins for Q58EU8 (Mus musculus)
Go to UniProtKB:  Q58EU8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IG ANTIBODY D2.3 (HEAVY CHAIN)
H
222Mus musculusGene Names: Ighg
Find proteins for P01863 (Mus musculus)
Go to UniProtKB:  P01863
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PDE
Query on PDE

Download SDF File 
Download CCD File 
L
PARA-NITROPHENYL PHOSPHONOBUTANOYL D-ALANINE
C13 H17 N2 O8 P
KBXXIYHMPQZHCH-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.251α = 90.00
b = 78.251β = 90.00
c = 158.805γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance