CROSSREACTIVE BINDING OF A CIRCULARIZED PEPTIDE TO AN ANTI-TGFALPHA ANTIBODY FAB-FRAGMENT


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B-Cell Epitope
Epitope  
   
Complex PDB ID 1E4X
Accession Number 3DIEP0027
IEDB ID 108202
Epitope Sequence P: V1; V2; S3; H4; F5; N6; D7
Starting Position1
Ending Position7
Epitope Type Linear Epitope

Assay Information  
Assay Antigen VVSHFND
PDB CategoryIMMUNE SYSTEM
Keyword IMMUNE SYSTEM; COMPLEX (ANTIBODY/ANTIGEN); CROSS-REACTIVITY; PROTEIN-PEPTIDE RECOGNITION
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 ChainP
Contact Area for Antigen there are large differences in the main chain conformations. Whereas in both structures a β-turn is formed and stabilized by a hydrogen bond
Contact Area for Antibody in TGFα this includes residues P1-P4
Comments[ P1: V1 P2: V2 P3: S3 P4: H4 P5: F5 P6: N6 P7: D7 ] The antibody binding site is a cleft with a deep central depression; where the side chains of residues P3 and P4 are accommodated. The epitope forms a common type I ß-turn including the residues P4-P7. All six CDR loops contact the epitope. Conformational comparison between tAb2 Fab/e-pep (this structure); tAb2 Fab/hc-pep2 [PDB: 1E4W] and unbound TGFa [PDB: 2TGF] showed that the Fab molecules have only small shifts of side chains. Epitope residues P3-P6 are very similar. Also; the side chains of the two P7 residues are at similar positions. In the hc-pep2 complex; the epitope main chain is shifted away from the Fab fragment; compared to e-pep. This happens to prevent a steric clash with the Fab fragment; due to the longer side chain of P7: E7 ; in hc-pep2. Comparing the e-pep conformation with the unbound TGFa; there are large differences in the main chain conformations. Whereas in both structures a ß-turn is formed and stabilized by a hydrogen bond; in TGFa this includes residues P1-P4; but in e-pep residues P4-P7.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
1.9
R-Value
Space Group
C 1 2 1
Unit Cell
Length(Å) Angle(°)
a = 173.82 α = 90
b = 45.09 β = 99.13
c = 120.41 γ = 90



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Source Information  
Structure Determination Method X-RAY DIFFRACTION
Source Organism MUS MUSCULUS
Common NameHOUSE MOUSE
Taxonomic ID10090
Source Organism MUS MUSCULUS
Common NameHOUSE MOUSE
Taxonomic ID10090
Source Organism MUS MUSCULUS
Common NameHOUSE MOUSE
Taxonomic ID10090
Entity ID2


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Ligand non-polymer