5ACM

Mcg immunoglobulin variable domain with methylene blue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain.

Brumshtein, B.Esswein, S.R.Salwinski, L.Phillips, M.L.Ly, A.T.Cascio, D.Sawaya, M.R.Eisenberg, D.S.

(2015) Elife 4: e10935-e10935

  • DOI: 10.7554/eLife.10935
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Overproduction of immunoglobulin light chains leads to systemic amyloidosis, a lethal disease characterized by the formation of amyloid fibrils in patients' tissues. Excess light chains are in equilibrium between dimers and less stable monomers which ...

    Overproduction of immunoglobulin light chains leads to systemic amyloidosis, a lethal disease characterized by the formation of amyloid fibrils in patients' tissues. Excess light chains are in equilibrium between dimers and less stable monomers which can undergo irreversible aggregation to the amyloid state. The dimers therefore must disassociate into monomers prior to forming amyloid fibrils. Here we identify ligands that inhibit amyloid formation by stabilizing the Mcg light chain variable domain dimer and shifting the equilibrium away from the amyloid-prone monomer.


    Organizational Affiliation

    UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, United States.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, United States.,Department of Biological Chemistry, Howard Hughes Medical Institute, UCLA, Los Angeles, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MCG
A, B
111Homo sapiensMutation(s): 0 
Gene Names: IGLV2-8
Find proteins for P01709 (Homo sapiens)
Go to UniProtKB:  P01709
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MBT
Query on MBT

Download SDF File 
Download CCD File 
A
3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM
METHYLENE BLUE
C16 H18 N3 S
RBTBFTRPCNLSDE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.110 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.220α = 90.00
b = 31.080β = 90.09
c = 73.630γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Data collection