SMTL ID : 8elh.1

Crystal Structure of HLA-B*15:01 in complex with spike derived peptide NQKLIANQF from SARS-CoV-2 virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASN- GLN- LYS- LEU- ILE- ALA- ASN- GLN- PHE: Spike protein S2'(Non-covalent)

ASN-GLN-LYS-LEU-ILE-ALA-ASN-GLN-PHE.1: 30 residues within 4Å: Chain A: Y.7, Y.9, M.45, Y.59, R.62, E.63, I.66, S.67, T.69, N.70, T.73, E.76, S.77, N.80, Y.84, R.97, Y.99, S.116, Y.123, T.143, K.146, W.147, A.150, E.152, Q.155, W.156, Y.159, L.163, W.167, Y.171 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.9, A:I.66, A:T.69, A:E.76, A:Y.99, A:Y.123, A:T.143, A:W.156, A:Y.159, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Y.9, A:Y.59, A:R.62, A:R.62, A:E.63, A:E.63, A:S.67, A:N.70, A:N.70, A:E.76, A:S.77, A:N.80, A:Y.99, A:Y.99, A:T.143, A:Q.155, A:Q.155, A:Y.159, A:Y.171 Salt bridges: A:K.146 pi-Stacking: A:W.147

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.10, S.11, H.13, P.14 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.11, A:Q.242 Water bridges: B:A.15 Hydrophobic interactions: A:W.204, A:L.206 Salt bridges: A:R.234

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 10 residues within 4Å: Chain A: G.1, S.2, H.3, D.29, L.179, Q.180, R.181, A.182, P.210, E.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.1, A:G.1, A:D.29 Water bridges: A:S.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Augusto, D.G. et al., A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature (2023)

Release Date

2023-06-14

Peptides

heavy chain HLA-B*15:01: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

heavy chain HLA-B*15:01

Beta-2-microglobulin

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