SMTL ID : 8roo.1

Crystal structure of HLA B*18:01 in complex with YERMCNIL, an 8-mer epitope from Influenza A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TYR- GLU- ARG- MET- CYS- ASN- ILE- LEU: Influenza A derived peptide/Nucleoprotein(Non-covalent)

TYR-GLU-ARG-MET-CYS-ASN-ILE-LEU.1: 30 residues within 4Å: Chain A: Y.7, H.9, S.24, E.58, Y.59, R.62, N.63, Q.65, I.66, S.67, T.69, N.70, T.73, Y.74, E.76, S.77, N.80, Y.84, L.95, R.97, Y.99, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, W.167 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.59, A:R.62, A:I.66, A:T.73, A:E.76, A:L.95, A:Y.99, A:Y.123, A:W.147, A:Y.159, A:W.167 Hydrogen bonds: A:S.24, A:E.58, A:N.63, A:N.70, A:N.70, A:T.73, A:S.77, A:N.80, A:Y.84, A:R.97, A:Y.99, A:Y.99, A:Q.155, A:Q.155, A:W.167 Water bridges: A:S.24, A:N.63, A:S.67, A:R.97, A:D.114 Salt bridges: A:H.9, A:K.146 pi-Cation interactions: A:R.62

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

EDO.2: 7 residues within 4Å: Chain A: D.122, Y.123, I.124, A.125, T.134, A.135, A.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.123, A:A.125 EDO.3: 5 residues within 4Å: Chain A: R.6, F.8, M.98 Chain B: S.58, K.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.58 EDO.4: 7 residues within 4Å: Chain A: Y.85, Y.118, K.121, D.122, Y.123, A.136, D.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.85, A:D.122 Water bridges: A:D.119 EDO.5: 4 residues within 4Å: Chain A: R.14, R.17, R.21 Chain B: D.35 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.35, A:R.14, A:R.17, A:R.17 EDO.6: 3 residues within 4Å: Chain A: E.229, L.230, V.231 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.229, A:E.229 Water bridges: A:L.230, A:L.230, A:V.231 EDO.7: 3 residues within 4Å: Chain A: R.79, R.82, G.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.82, A:R.82, A:G.83 EDO.8: 2 residues within 4Å: Chain A: A.40, A.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.41 EDO.12: 2 residues within 4Å: Chain A: R.21 Chain B: H.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.21 Water bridges: A:D.37 EDO.13: 5 residues within 4Å: Chain B: K.42, E.70, F.71, T.72, Y.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.70, B:T.72, B:Y.79

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain A: L.78, R.82, H.93, Y.118 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.78, A:Y.118, H2O.5

3 x K: POTASSIUM ION(Non-covalent)

K.10: 1 residues within 4Å: Chain A: K.68 No protein-ligand interaction detected (PLIP) K.15: 1 residues within 4Å: Chain B: S.21 No protein-ligand interaction detected (PLIP) K.16: 3 residues within 4Å: Chain B: E.37, D.39, R.82 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.39

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 2 residues within 4Å: Chain A: S.88, E.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.89

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.14: 2 residues within 4Å: Chain B: S.58, K.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leong, S.L. et al., Characterisation of novel influenza-derived HLA-B*18:01-restricted epitopes. Clin Transl Immunology (2024)

Release Date

2024-05-08

Peptides

MHC class I antigen: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

MHC class I antigen

Beta-2-microglobulin

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