Crystal structure of the engineered neutralizing antibody M18 complexed with anthrax protective antigen domain 4


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B-Cell Epitope
Epitope  
   
Complex PDB ID 3ETB
Accession Number 3DIEP0203
IEDB ID 104696
Epitope Sequence D648; L652; D658; D683; K684; L685; P686; Y688
Starting Position648,652,658,683-686,688
Ending Position688
Epitope Type Discontinuous Epitope

Assay Information  
Assay Antigen protective antigen Bacillus anthracis
PDB CategoryIMMUNE SYSTEM/TOXIN
Keyword single-chain FV; monoclonal antibody; immunoglobulin; toxin; antibody-antigen complex; IMMUNE SYSTEM/TOXIN COMPLEX
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain F
Antibody Chain 2 PDB ChainF
Antigen PDB ChainJ
Contact Area for Antigen 896.9
Contact Area for Antibody821.4
CommentsAll of the antibody CDR loops; except L3; make some direct contact with the epitope; but the strongest interactions are made with H3 and L2. There are three main contact loops of the an the antigen.Conformational comparison between M18 scFv/PAD4 (this structure); CMG2 (anthrax toxin receptor)/PAD4 [PDB: 1T6B] and unbound PA [PDB: 1ACC] showed that the PAD4 domain complexed with antibody is virtually identical with that of the unbound PAD4; indicating that antibody binding does not cause significant conformational change in the antigen. Comparing the M18/PAD4 and CMG2/PAD4 structures; the two binding interfaces overlap well. The CMG2 receptor interacts with the same three binding loops of PAD4 observed to make antibody contacts. One conformational difference in the CMG2/PAD4 binding interface is the insertion of the CMG2 residue V115 side chain into a pronounced hydrophobic “socket” of PAD4. In contrast; in the M18/PAD4 complex; this same PAD4 hydrophobic socket is not occupied by any antibody residue.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
3.8
R-Value
0.232
Space Group
P 1 21 1
Unit Cell
Length(Å) Angle(°)
a = 48.94 α = 90
b = 299.72 β = 94.45
c = 68.95 γ = 90


Source Information  
Structure Determination Method X-RAY DIFFRACTION


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Ligand
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