Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES)


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B-Cell Epitope
Epitope  
   
Complex PDB ID 1P7K
Accession Number 3DIEP0147
IEDB ID 76911
Epitope Sequence biological buffer HEPES; 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid
Starting Position901
Ending Position1201
Epitope Type Non peptidic

Assay Information  
Assay Antigen biological buffer HEPES; 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid
PDB CategoryIMMUNE SYSTEM
Keyword FAB; ANTIBODY; ANTI-DNA ANTIBODY; AUTOANTIBODY; LUPUS; HEPES; IMMUNE SYSTEM
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain H
Antibody Chain 2 PDB ChainL
Antigen PDB ChainL
Contact Area for Antigen 252.7
Contact Area for Antibody157.3
CommentsDespite the chemical and structural difference of two ligand; the HEPES binding site of Fab DNA-1 (this structure) and its dT5 binding site [PDB: 1I8M] are similar in terms of CDR usage and paratope residues. While they differ in shape and size due to large conformational changes in CDR H3 that result in movement of TyrH100A of 13 Ã… (based on the hydroxyl).

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
1.75
R-Value
0.197
Space Group
P 21 21 2
Unit Cell
Length(Å) Angle(°)
a = 107.666 α = 90
b = 156.703 β = 90
c = 61.003 γ = 90


Source Information  
Structure Determination Method X-RAY DIFFRACTION


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Ligand
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