HLA-DR1 (DRA; DRB1 0101) HUMAN CLASS II HISTOCOMPATIBILITY PROTEIN (EXTRACELLULAR DOMAIN) COMPLEXED WITH ENDOGENOUS PEPTIDE


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MHC-Binding
Epitope  
   
Complex PDB ID 1AQD
Accession Number 3DIEP0398
IEDB ID 68791
Epitope Sequence VGSDWRFLRGYHQYA
Starting Position2
Ending Position15
Epitope Type Linear Epitope

Assay Information  
Assay Antigen "Purified MHC - X-ray crystallography Structure (crystal; NMR; etc.)"
PDB CategoryCOMPLEX (MHC PROTEIN/ANTIGEN)
Keyword COMPLEX (MHC PROTEIN/ANTIGEN); HISTOCOMPATIBILITY ANTIGEN
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain G
Antigen PDB ChainI
CommentsThe asymmetric unit contains four molecules. Each one has a HLA-DR1 dimer complexed with the epitope peptide. The four complexes are arranged as two copies of essentially the same (ab)2 dimer: complex I: ?-chain A; ?-chain B; peptide C; complex II: ?-chain D; ?-chain E; peptide F; complex III: ?-chain G; ?-chain H; peptide I; complex IV: ?-chain J; ?-chain K; peptide L. Complex III is the most well defined. The first epitope residue (V1) is disordered in all four complexes and coordinates are not included in the model. Complexes I; III and IV contain the same residues in each chain and complex II is also missing the second epitope residue (G2). Since complex III is the most well defined; it has the best model. Thus; it will be the only one curated.The sidechain of epitope residue P7: Y11 is found in two different orientations in different complexes in the asymmetric unit.Water molecules were added in the model based on outputs from the CCP4 suite of programs and ARP. There are three water molecules underneath the peptide in the region between pockets 6 and 7; which form a network that is variously occupied in the four complexes.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
2.45
R-Value
0.216
Space Group
C 1 2 1
Unit Cell
Length(Å) Angle(°)
a = 134.514 α = 90
b = 134.32 β = 104.82
c = 131.232 γ = 90



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Source Information  
Structure Determination Method X-RAY DIFFRACTION