SMTL ID : 6hby.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: T.40, W.42, S.52, F.53 Chain C: R.3 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.3, A:F.53, A:F.53 EDO.2: 6 residues within 4Å: Chain A: I.81, N.83 Chain B: T.4, R.5, P.6, R.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.7, B:R.7, A:N.83 EDO.3: 5 residues within 4Å: Chain A: F.107, R.145 Chain B: L.148, I.149, Q.150 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.145, B:Q.150 EDO.4: 6 residues within 4Å: Chain A: I.7, D.24, G.27, P.138, R.139, E.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.139 EDO.5: 2 residues within 4Å: Chain B: L.110, Q.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.111 EDO.6: 2 residues within 4Å: Chain B: Q.111, H.112 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain A: I.81, T.82 Chain B: Y.33, N.34, Q.35, E.36 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.33, B:Q.35, A:T.82, A:T.82, A:T.82 EDO.8: 4 residues within 4Å: Chain A: N.93, Y.149 Chain B: N.151, D.153 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.153, A:N.93 Water bridges: B:T.155, A:R.43 EDO.9: 6 residues within 4Å: Chain A: H.142 Chain B: Q.35, E.36, E.37, V.51, T.52 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.37, A:H.142

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

PO4.10: 2 residues within 4Å: Chain B: H.112, H.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.113 Salt bridges: B:H.112, B:H.113 PO4.11: 4 residues within 4Å: Chain B: P.179, S.180, V.181, T.182 No protein-ligand interaction detected (PLIP)

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
D

B
E

C
F

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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