4ONG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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:  
    4ONF, 4ONG

  • 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 to target for treatment, and the mechanism of action underlying immunotherapy ...

    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

    Elan Pharmaceuticals, Inc. 300 Technology Sq., Cambridge, MA 02139, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3D6 FAB ANTIBODY HEAVY CHAINA [auth H]222Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
3D6 FAB ANTIBODY LIGHT CHAINB [auth L]219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Amyloid beta A4 proteinC [auth P]40Homo sapiensMutation(s): 0 
Gene Names: APPA4AD1
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05067
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
LA [auth L],
Q [auth H],
R [auth H]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth L],
BA [auth L],
CA [auth L],
D [auth H],
DA [auth L],
AA [auth L],
BA [auth L],
CA [auth L],
D [auth H],
DA [auth L],
E [auth H],
EA [auth L],
F [auth H],
FA [auth L],
G [auth H],
GA [auth L],
H,
HA [auth L],
I [auth H],
IA [auth L],
J [auth H],
JA [auth L],
K [auth H],
KA [auth L],
L [auth H],
M [auth H],
N [auth H],
O [auth H],
P [auth H],
X [auth L],
Y [auth L],
Z [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
MA [auth L],
NA [auth L],
OA [auth L],
PA [auth L],
QA [auth L],
MA [auth L],
NA [auth L],
OA [auth L],
PA [auth L],
QA [auth L],
RA [auth L],
S [auth H],
T [auth H],
U [auth H],
V [auth H],
W [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.04α = 90
b = 84.94β = 90
c = 175.69γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
COMOphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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