SMTL ID : 8ye4.1 (1 other biounit)

The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ASN- TYR- ASN- TYR- LEU- TYR- ARG- LEU- PHE: Spike protein S1(Non-covalent)

ASN-TYR-ASN-TYR-LEU-TYR-ARG-LEU-PHE.1: 41 residues within 4Å: Chain A: M.5, Y.7, F.22, A.24, M.45, Y.59, E.62, E.63, K.66, V.67, H.70, T.73, E.76, N.77, I.80, Y.84, L.95, M.97, F.99, H.114, Y.116, Y.123, T.143, K.146, W.147, A.150, V.152, Q.155, Q.156, Y.159, T.163, G.167, Y.171 Chain C: A.27, Q.29, S.30, N.89, Y.97 Chain D: T.95, G.97, Y.98 43 PLIP interactions: 33 interactions with chain A, 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: A:Y.7, A:K.66, A:K.66, A:V.67, A:H.70, A:E.76, A:N.77, A:I.80, A:I.80, A:L.95, A:F.99, A:W.147, A:V.152, A:Y.159, A:T.163, D:T.95, D:Y.98, D:Y.98, C:Y.97 Hydrogen bonds: A:Y.7, A:E.63, A:E.63, A:K.66, A:H.70, A:T.73, A:N.77, A:N.77, A:Y.84, A:K.146, A:Q.155, A:Q.155, A:Q.156, A:Y.159, A:Y.171, D:Y.98, D:Y.98, C:S.30, C:S.30, C:N.89 pi-Stacking: A:F.99, A:Y.116, A:Y.123 pi-Cation interactions: D:Y.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, S. et al., Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants. J.Biol.Chem. (2024)

Release Date

2024-08-21

Peptides

MHC class I antigen precusor: A
Beta-2-microglobulin: B
TCR NYN-I alpha chain: C
TCR NYN-I beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

D
H

MHC class I antigen precusor

Beta-2-microglobulin

TCR NYN-I alpha chain

TCR NYN-I beta chain

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