1QAC

CHANGE IN DIMERIZATION MODE BY REMOVAL OF A SINGLE UNSATISFIED POLAR RESIDUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Change in dimerization mode by removal of a single unsatisfied polar residue located at the interface.

Pokkuluri, P.R.Cai, X.Johnson, G.Stevens, F.J.Schiffer, M.

(2000) Protein Sci. 9: 1852-1855

  • DOI: 10.1110/ps.9.9.1852
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The importance of unsatisfied hydrogen bonding potential on protein-protein interaction was studied. Two alternate modes of dimerization (conventional and flipped form) of an immunoglobulin light chain variable domain (V(L)) were previously identifie ...

    The importance of unsatisfied hydrogen bonding potential on protein-protein interaction was studied. Two alternate modes of dimerization (conventional and flipped form) of an immunoglobulin light chain variable domain (V(L)) were previously identified. In the flipped form, interface residue Gln89 would have an unsatisfied hydrogen bonding potential. Removal of this Gln should render the flipped dimer as the more favorable quaternary form. High resolution crystallographic studies of the Q89A and Q89L mutants show, as we predicted, that these proteins indeed form flipped dimers with very similar interfaces. A small cavity is present in the Q89A mutant that is reflected in the approximately 100 times lower association constant than found for the Q89L mutant. The association constant of Q89A and Q89L proteins (4 x 10(6) M(-1) and >10(8) M(-1)) are 10- and 1,000-fold higher than that of the wild-type protein that forms conventional dimers clearly showing the energetic reasons for the flipped dimer formation.


    Related Citations: 
    • A domain flip as a result of a single amino-acid substitution.
      Pokkuluri, P.R.,Huang, D.-B.,Raffen, R.,Cai, X.,Johnson, G.,Wilkins Stevens, P.,Stevens, F.J.,Schiffer, M.
      (1998) Structure 6: 1067


    Organizational Affiliation

    Argonne National Laboratory, Biosciences Division, Illinois 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN
A, B
114Homo sapiensMutation(s): 0 
Gene Names: IGKV4-1
Find proteins for P06312 (Homo sapiens)
Go to UniProtKB:  P06312
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.300α = 90.00
b = 83.600β = 109.00
c = 42.800γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description