Figure 3.
Fig. 3. A type II -turn at the C-terminal
region of the Gag[PP16] peptide. (A) C-terminal region of the
DR1 peptide-binding site with bound Gag[PP16] peptide showing
conserved MHC peptide hydrogen bonds. Conserved MHC peptide
hydrogen bonds in this region are shown as gray dashed lines,
with the Gag[PP16] intraturn hydrogen bond between the nitrogen
of Ala (P12) and the carbonyl oxygen of Ser (P9) shown as a red
dashed line. (B) Closeup view of the Gag[PP16] hairpin, showing
the intraturn hydrogen bond and - values characteristic of
a type II -turn. (C) Alignment of
HLA-DR crystal structures exhibiting ordered peptide density
beyond P10. Complexes were aligned by least-squares fitting of
1
and 1 domains. Peptides are
shown as C traces. DR1/TP1 is red
(PDB ID code 1KLU [PDB]
), DR2a/MBP is blue (PDB ID code 1FV1 [PDB]
), DR3/CLIP is magenta (PDB ID code 1A6A [PDB]
), DR1/Ha is cyan (PDB ID code 1DLH [PDB]
), DR2a/EBV is gray (PDB ID code 1H15 [PDB]
), and DR4/collagen is orange (PDB ID code 2SEB [PDB]
).
-turn at the C-terminal
region of the Gag[PP16] peptide. (A) C-terminal region of the
DR1 peptide-binding site with bound Gag[PP16] peptide showing
conserved MHC peptide hydrogen bonds. Conserved MHC peptide
hydrogen bonds in this region are shown as gray dashed lines,
with the Gag[PP16] intraturn hydrogen bond between the nitrogen
of Ala (P12) and the carbonyl oxygen of Ser (P9) shown as a red
dashed line. (B) Closeup view of the Gag[PP16] hairpin, showing
the intraturn hydrogen bond and 
- 
values characteristic of
a type II 
1
and