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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.