SMTL ID : 6hby.1 (1 other biounit)

HLA class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-1-mer

Ligands

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: Y.77, P.79 Ligand excluded by PLIP EDO.2: 2 residues within 4Å: Chain A: T.81, N.82 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: N.82, W.166 Chain B: T.4, R.5, R.7 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: I.6, D.23, G.26, P.137, R.138, E.139 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: T.39, W.41, S.51, F.52 Chain C: R.3 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain B: R.40, D.42, R.49 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: Y.61, W.62, Q.65 Chain C: L.12, N.13 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: I.80, T.81 Chain B: Y.33, N.34, Q.35, E.36 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: T.78, Y.79 Chain C: A.7, E.8, L.9 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: L.68, Q.71, R.72 Chain C: L.9 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain B: R.24, V.25, V.76, R.81 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: H.112, H.113, P.166 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: N.92, V.102, Y.148 Chain B: D.153 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: F.24, D.25 Chain B: Y.124, P.125, G.126, F.156 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: F.49 Chain B: V.86, S.89 Chain C: P.4 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain B: R.40 Ligand excluded by PLIP

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 2 residues within 4Å: Chain A: K.109, R.138 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.109, A:R.138 PO4.18: 3 residues within 4Å: Chain B: E.47, K.66, R.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.47 Salt bridges: B:K.66, B:R.73 PO4.19: 5 residues within 4Å: Chain B: A.50, V.51, T.52, E.53, R.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.50 Water bridges: B:E.53 Salt bridges: B:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

MacLachlan, B.J. et al., Human leukocyte antigen (HLA) class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope. J.Biol.Chem. (2019)

Release Date

2019-08-14

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA class II histocompatibility antigen, DRB1-1 beta chain: B
ARRPPLAELAALNLSGSRL 5T4 tumour epitope: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1-1 beta chain

ARRPPLAELAALNLSGSRL 5T4 tumour epitope

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