Table 5.
Available X-ray structures of peptide - class II MHC complexes in the Protein Data Bank.
| MHC Allele | PDB Entry | Peptide Sequence |
|---|---|---|
| DRB1*0101 | 1AQD | VGSDWRFLRGYHQYA |
| DRB1*0101 | 1DLH, 2G9H |
PKYVKQNTLKLAT |
| DRB1*0101 | 1KLG | GELIGILNAAKVPAD |
| DRB1*0101 | 1KLU | GELIGTLNAAKVPAD |
| DRB1*0101 | 1SJE | PEVIPMFSALSEGATP |
| DRB1*0101 | 1T5W | AAYSDQATPLLLSPR |
| DRB1*0101 | 2FSE | AGFKGEQGPKGEPG |
| DRB1*0301 | 1A6A | LPKPPKPVSKMRMATPLLMQALPM |
| DRB1*0401 | 1J8H | PKYVKQNTLKLAT |
| DRB1*0401 | 2SEB | QYMRADQAAGGLR |
| DRB1*1501 | 1BX2 | ENPVVHFFKNIVTPR |
| DRB3*0101 | 2Q6W | AWRSDEALPLGS |
| DRB5*0101 | 1FV1 | NPVVHFFKNIVTPRTPPPSQ |
| DRB5*0101 | 1H15 | GGVYHFVKKHVHES |
| H2-IAb | 1LNU | FEAQKAKANKAVD |
| H2-IAb | 1MUJ | LPKPPKPVSKMRMATPLLMQALPM |
| H2-IAd | 1IAO | RGISQAVHAAHAEINEAGR |
| H2-IAd | 2IAD | RGHNTNGVTAASSHE |
The 9-residue core segment of the peptide that binds to the MHC molecule, which begins with the P1 residue, is highlighted in boldface in the peptide sequence. These structures show which peptide segment binds to the MHC molecule and so are used to evaluate how well the RTA method predicts the correct peptide binding register.