COMPLEX BETWEEN FV ANTIBODY FRAGMENT AND AN ANALOGUE OF THE MAIN IMMUNOGENIC REGION OF THE ACETYLCHOLINE RECEPTOR


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B-Cell Epitope
Epitope  
   
Complex PDB ID 1F3R
Accession Number 3DIEP0035
IEDB ID 130336
Epitope Sequence WNPGDYGGIL
Starting Position67
Ending Position75
Epitope Type Linear Sequence:A: W67; N68; P69; G70; D71; Y72; G73; G74; I75; (NLE)76

Assay Information  
Assay Antigen WNPGDYGGIL + NLeu(L10)
PDB CategoryIMMUNE SYSTEM
Keyword IG-FOLD; IMMUNO COMPLEX; ANTIBODY-ANTIGEN; BETA-TURN; IMMUNE SYSTEM
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain B
Antigen PDB ChainA
Contact Area for Antigen 765.6
Contact Area for Antibody596.3
CommentsThe complex between the epitope and the scFv198 antibody fragment was described based on two-dimensional nmr experiments and molecular modeling of the antibody chain. The epitope is characterized by a tight ß-turn-like N-terminal loop and a C-terminal bent. The complex between the epitope and scFv198 is stabilized by 12 intermolecular hydrogen bonds; two central ionic interactions; and 38 van der Waals contacts. The Trp at position 1 (W67) makes 3 hydrogen bonds and 10 van der Waals contacts and occupies a hydrophobic pocket in the binding site. The Asn at position 2 (N68) makes 2 hydrogen bonds and 3 van der Waals contacts. The Gly at position 4 (G70) makes 2 hydrogen bonds and 1 van der Waals contact. The Asp at position 5 (D71) makes 1 hydrogen bond and 5 van der Waals contacts and is exposed to the positively charged bottom of the binding site. The Tyr at position 6 (Y72) makes 1 hydrogen bond. The Gly at position 8 (G74) makes 2 hydrogen bonds. The Ile at position 9 (I75) makes 1 hydrogen bond and occupies a hydrophobic pocket in the binding site. The Pro position 3 has no contacts with the antibody.

Experimental Details
Experimental Method
SOLUTION NMR
Classification:
refinement
Refrences details:
This structure was determined using standard 2D homonuclear techniques.
Software:
DISCOVER3 97
Manufacturer:
Bruker


Source Information  
Structure Determination Method SOLUTION NMR
Source Organism Rattus norvegicus
Common NameNorway rat
Taxonomic ID10116
Entity ID2

Ligand L-peptide linking




Sequence
Protein Name
COMPLEX BETWEEN FV ANTIBODY FRAGMENT AND AN ANALOGUE OF THE MAIN IMMUNOGENIC REGION OF THE ACETYLCHOLINE RECEPTOR
Poly type
polypeptide(L)
Sequence status
Complete

Err:Conn