4ONG

Fab fragment of 3D6 in complex with amyloid beta 1-40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure reveals conservation of amyloid-beta conformation recognized by 3D6 following humanization to bapineuzumab.

Feinberg, H.Saldanha, J.W.Diep, L.Goel, A.Widom, A.Veldman, G.M.Weis, W.I.Schenk, D.Basi, G.S.

(2014) Alzheimers Res Ther 6: 31-31

  • DOI: 10.1186/alzrt261
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Immunotherapy targeting amyloid-β peptide is under active clinical investigation for treatment of Alzheimer's disease (AD). Among the hypotheses being investigated for impact on clinical outcome are the preferred epitope or conformation of amyloid-β ...

    Immunotherapy targeting amyloid-β peptide is under active clinical investigation for treatment of Alzheimer's disease (AD). Among the hypotheses being investigated for impact on clinical outcome are the preferred epitope or conformation of amyloid-β to target for treatment, and the mechanism of action underlying immunotherapy. Bapineuzumab (humanized 3D6), a neo-epitope specific antibody recognizing amyloid-β1-5 with strong preference for an exposed Asp residue at the N-terminus of the peptide, has undergone advanced clinical testing for treatment of AD.


    Organizational Affiliation

    Departments of Structural Biology and of Molecular & Cellular Physiology, 299 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305, USA.,Elan Pharmaceuticals, Inc. 300 Technology Sq., Cambridge, MA 02139, USA.,Pfizer, Cambridge, MA, USA.,Prothena Biosciences, Inc., 650 Gateway Blvd., San Francisco, CA 94080, USA.,Abbvie Bioresearch Center, Worcester, MA, USA.,National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3D6 FAB ANTIBODY HEAVY CHAIN
H
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3D6 FAB ANTIBODY LIGHT CHAIN
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Amyloid beta A4 protein
P
40Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
H, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
H, L
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
H, L
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.177 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 40.040α = 90.00
b = 84.940β = 90.00
c = 175.690γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXrefinement
COMOphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description