SMTL ID : 7n1e.1

SARS-CoV-2 RLQ peptide-specific TCR pRLQ3 binds to RLQ-HLA-A2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ARG- LEU- GLN- SER- LEU- GLN- THR- TYR- VAL: Spike protein S2(Non-covalent)

ARG-LEU-GLN-SER-LEU-GLN-THR-TYR-VAL.1: 39 residues within 4Å: Chain A: Y.7, F.9, M.45, E.63, K.66, V.67, A.69, H.70, T.73, D.77, T.80, L.81, Y.84, R.97, Y.99, Y.116, T.143, W.147, V.152, Q.155, L.156, Y.159, T.163, W.167, Y.171 Chain C: S.29, F.91, N.92, N.93, A.94, G.95, N.96 Chain D: Q.48, V.53, G.95, G.96, A.97, G.98, A.100 44 PLIP interactions: 28 interactions with chain A, 4 interactions with chain D, 12 interactions with chain C Hydrophobic interactions: A:Y.7, A:Y.7, A:F.9, A:V.67, A:T.73, A:D.77, A:L.81, A:Y.116, A:V.152, A:Q.155, A:Y.159, A:Y.159, A:W.167, D:Q.48, D:A.100, C:F.91, C:F.91 Hydrogen bonds: A:Y.7, A:E.63, A:K.66, A:T.73, A:D.77, A:Y.84, A:R.97, A:R.97, A:Y.99, A:Y.99, A:T.143, A:Y.159, A:W.167, A:Y.171, D:G.96, C:S.29, C:S.29, C:N.92, C:N.93, C:G.95, C:N.96, C:N.96, C:N.96 Water bridges: A:H.70, D:Q.48, C:S.29, C:G.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, D. et al., Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and private T-cell receptors. Nat Commun (2022)

Release Date

2021-07-28

Peptides

MHC class I antigen, A-2 alpha chain: A
Beta-2-microglobulin: B
pRLQ3 T cell receptor alpha chain: C
pRLQ3 T cell receptor beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

MHC class I antigen, A-2 alpha chain

Beta-2-microglobulin

pRLQ3 T cell receptor alpha chain

pRLQ3 T cell receptor beta chain

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