SMTL ID : 8rbv.1

SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by HLA-A*02:01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VAL- LEU- ASN- ASP- ILE- LEU- ALA- ARG- LEU: SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant(Non-covalent)

VAL-LEU-ASN-ASP-ILE-LEU-ALA-ARG-LEU.1: 28 residues within 4Å: Chain A: M.29, Y.31, F.33, M.69, Y.83, E.87, R.89, K.90, V.91, H.94, T.97, D.101, T.104, L.105, Y.108, R.121, Y.123, Y.140, T.167, K.170, W.171, V.176, Q.179, L.180, Y.183, T.187, W.191, Y.195 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:Y.31, A:F.33, A:Y.83, A:K.90, A:V.91, A:H.94, A:D.101, A:T.104, A:L.105, A:L.105, A:Y.108, A:Y.140, A:T.167, A:V.176, A:Q.179, A:Y.183, A:T.187, A:W.191, A:W.191 Hydrogen bonds: A:E.87, A:D.101, A:Y.108, A:Y.123, A:Y.123, A:T.167, A:K.170, A:Y.195, A:Y.195 Water bridges: A:K.90, A:K.90, A:D.101, A:R.121, A:R.121, A:R.121 Salt bridges: A:R.89, A:K.170

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

ACT.2: 5 residues within 4Å: Chain A: R.30, F.32, D.53, D.54 Ligands: PEG.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.32 Hydrogen bonds: A:D.54 Water bridges: A:S.28, A:R.30 Salt bridges: A:R.30 ACT.6: 8 residues within 4Å: Chain A: W.228, L.230, R.258, Q.266 Chain B: S.12, R.13, H.14, P.15 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.12, A:Q.266 Water bridges: B:A.16

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

EDO.3: 4 residues within 4Å: Chain A: R.30, M.122, R.135 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.30, A:R.135 EDO.7: 5 residues within 4Å: Chain B: V.10, K.95, W.96, D.97, M.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.97 Water bridges: B:V.10

2 x CD: CADMIUM ION(Non-covalent)

CD.4: 2 residues within 4Å: Chain A: H.215, H.216 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.215, A:H.215 CD.5: 1 residues within 4Å: Chain A: H.169 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.169

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

PEG.8: 9 residues within 4Å: Chain A: F.32, M.122, Q.139 Chain B: F.57, S.58, K.59, W.61 Ligands: ACT.2, EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahn, Y.M. et al., The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific. Curr Res Struct Biol (2024)

Release Date

2024-05-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HLA class I antigen

Beta-2-microglobulin

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