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 
  • R-Value Observed: 0.111 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.7554/eLife.10935
  • Primary Citation of Related Structures:  
    5ACL, 5ACM

  • 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 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

    Department of Biological Chemistry, Howard Hughes Medical Institute, UCLA, Los Angeles, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MCG
A, B
111Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01709 (Homo sapiens)
Explore P01709 
Go to UniProtKB:  P01709
GTEx:  ENSG00000278196 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01709
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MBT
Query on MBT

Download Ideal Coordinates CCD File 
C [auth A]3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM
C16 H18 N3 S
RBTBFTRPCNLSDE-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.122 
  • R-Value Work: 0.110 
  • R-Value Observed: 0.111 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.22α = 90
b = 31.08β = 90.09
c = 73.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description