3OVJ

Structure of an amyloid forming peptide KLVFFA from amyloid beta in complex with orange G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Towards a pharmacophore for amyloid.

Landau, M.Sawaya, M.R.Faull, K.F.Laganowsky, A.Jiang, L.Sievers, S.A.Liu, J.Barrio, J.R.Eisenberg, D.

(2011) Plos Biol. 9: e1001080-e1001080

  • DOI: 10.1371/journal.pbio.1001080
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Diagnosing and treating Alzheimer's and other diseases associated with amyloid fibers remains a great challenge despite intensive research. To aid in this effort, we present atomic structures of fiber-forming segments of proteins involved in Alzheime ...

    Diagnosing and treating Alzheimer's and other diseases associated with amyloid fibers remains a great challenge despite intensive research. To aid in this effort, we present atomic structures of fiber-forming segments of proteins involved in Alzheimer's disease in complex with small molecule binders, determined by X-ray microcrystallography. The fiber-like complexes consist of pairs of β-sheets, with small molecules binding between the sheets, roughly parallel to the fiber axis. The structures suggest that apolar molecules drift along the fiber, consistent with the observation of nonspecific binding to a variety of amyloid proteins. In contrast, negatively charged orange-G binds specifically to lysine side chains of adjacent sheets. These structures provide molecular frameworks for the design of diagnostics and drugs for protein aggregation diseases.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KLVFFA hexapeptide segment from Amyloid beta
A, B, C, D
6Homo sapiensMutation(s): 0 
Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens)
Go to Gene View: APP
Go to UniProtKB:  P05067
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ORA
Query on ORA

Download SDF File 
Download CCD File 
B, D
7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid
Orange G
C16 H12 N2 O7 S2
MPVDXIMFBOLMNW-ISLYRVAYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.205 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 9.536α = 62.28
b = 26.008β = 88.59
c = 25.803γ = 88.45
Software Package:
Software NamePurpose
SCALEPACKdata scaling
ADSCdata collection
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance