SMTL ID : 8z06.1

The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYDYWYRSF(JN.1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASN- TYR- ASP- TYR- TRP- TYR- ARG- SER- PHE: Spike protein S2'(Non-covalent)

ASN-TYR-ASP-TYR-TRP-TYR-ARG-SER-PHE.1: 32 residues within 4Å: Chain A: Y.7, F.22, A.24, M.45, Y.59, E.62, E.63, K.66, V.67, A.69, H.70, T.73, N.77, I.80, Y.84, L.95, M.97, F.99, H.114, Y.116, Y.123, T.143, K.146, W.147, V.152, Q.155, Q.156, Y.159, T.163, G.167, R.170, Y.171 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:Y.7, A:K.66, A:K.66, A:A.69, A:H.70, A:N.77, A:I.80, A:L.95, A:F.99, A:T.143, A:W.147, A:V.152, A:Y.159, A:T.163 Hydrogen bonds: A:Y.7, A:E.63, A:E.63, A:N.77, A:N.77, A:T.143, A:Q.155, A:Q.155, A:Q.156, A:Y.159, A:R.170, A:Y.171 Water bridges: A:Y.7, A:H.70 Salt bridges: A:K.146 pi-Stacking: A:F.99, A:H.114, A:Y.116, A:Y.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, J. et al., T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots. Nat.Immunol. (2025)

Release Date

2025-01-29

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MHC class I antigen

Beta-2-microglobulin

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