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Table 5 Available X-ray structures of peptide - class II MHC complexes in the Protein Data Bank.

From: Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model

MHC Allele PDB Entry Peptide Sequence
DRB1*0101 1AQD VGSDWRFLRGYHQ YA
DRB1*0101 1DLH,
2G9H
PKYVKQNTLKL AT
DRB1*0101 1KLG GELIGILNAAKV PAD
DRB1*0101 1KLU GELIGTLNAAKV PAD
DRB1*0101 1SJE PEVIPMFSALS EGATP
DRB1*0101 1T5W AAYSDQATPLL LSPR
DRB1*0101 2FSE AGFKGEQGPKG EPG
DRB1*0301 1A6A LPKPPKPVSKMRMATPLLM QALPM
DRB1*0401 1J8H PKYVKQNTLKL AT
DRB1*0401 2SEB QYMRADQAAGG LR
DRB1*1501 1BX2 ENPVVHFFKNIVT PR
DRB3*0101 2Q6W AWRSDEALPL GS
DRB5*0101 1FV1 NPVVHFFKNIVTPRT PPPSQ
DRB5*0101 1H15 GGVYHFVKKHVH ES
H2-IAb 1LNU FEAQKAKANKA VD
H2-IAb 1MUJ LPKPPKPVSKMRMATPLLM QALPM
H2-IAd 1IAO RGISQAVHAAHA EINEAGR
H2-IAd 2IAD RGHNTNGVTAASS HE
  1. 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.