5LVE

STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGHT CHAIN LEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 

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.,Stevens, P.W.,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
BENCE-JONES PROTEIN LEN
A
114Homo sapiensMutation(s): 1 
Gene Names: IGKV4-1
Find proteins for P06312 (Homo sapiens)
Go to UniProtKB:  P06312
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 106.300α = 90.00
b = 106.300β = 90.00
c = 45.100γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-18
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-06
    Type: Data collection, Database references