VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH AN AFFINITY MATURED ANTIBODY


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B-Cell Epitope
Epitope  
   
Complex PDB ID 1CZ8
Accession Number 3DIEP0019
IEDB ID 122246
Epitope Sequence V: F43; Y47 W: Y71; K74; Q105; I106; M107; R108; I109; K110; H112; Q113; G114; Q115; H116; I117; G118; E119; M120
Starting Position43,47,71,74,105
Ending Position110,112-120
Epitope Type Discontinuous Epitope

Assay Information  
Assay Antigen VEGF homodimer Homo sapiens
PDB CategoryIMMUNE SYSTEM
Keyword COMPLEX (ANTIBODY/ANTIGEN); CYSTINE KNOT; FAB FRAGMENT; 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,K
Antigen PDB ChainV
CommentsAntigen residues interacting with antibody; paratope residues and contacts are not provided in the reference. This structure is very similar to the structure of VEGF antigen with Fab-12 variant Y0192; the Fab of the wild-type humanized murine anti-VEGF mAb A4.6.1 [PDB: 1BJ1]. The Y0317 variant differ from the Y0192 variant at four amino acids of the heavy chain: T28D; N31H; H101Y; and S105T; The mutation H101Y introduces two additional hydrogen bonds between the antigen and the Fab and responsible for increase of antibody-antigen binding affinity by 14-fold.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
2.4
R-Value
0.208
Space Group
P 1 21 1
Unit Cell
Length(Å) Angle(°)
a = 89.12 α = 90
b = 66.4 β = 94.7
c = 138.75 γ = 90


Source Information  
Structure Determination Method X-RAY DIFFRACTION

Ligand
Ligand NameSULFATE ION
Chem Name SO4
Ligand NameSULFATE ION
Chem Name SO4




Sequence
Protein Name
SULFATE ION
Poly type
polypeptide(L)
Sequence status
Complete

Err:Conn