SMTL ID : 7p3e.1 (1 other biounit)

MHC I A02 Allele presenting YLQLRTFLL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TYR- LEU- GLN- LEU- ARG- THR- PHE- LEU- LEU: TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU(Non-covalent)

TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU.1: 30 residues within 4Å: Chain A: M.5, Y.7, F.9, M.45, E.63, K.66, V.67, H.70, T.73, V.76, D.77, T.80, L.81, Y.84, R.97, Y.99, H.114, Y.116, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, T.163, W.167, Y.171 Ligands: IOD.14 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:Y.7, A:F.9, A:K.66, A:V.67, A:V.76, A:D.77, A:L.81, A:Y.116, A:Y.116, A:Y.123, A:T.143, A:W.147, A:V.152, A:Q.155, A:L.156, A:Y.159, A:T.163, A:W.167, A:W.167 Hydrogen bonds: A:Y.7, A:E.63, A:D.77, A:T.80, A:Y.84, A:Y.99, A:Y.99, A:H.114, A:K.146, A:W.147, A:Q.155, A:Y.171, A:Y.171 Water bridges: A:H.70, A:D.77, A:R.97 Salt bridges: A:K.146 pi-Stacking: A:W.167 pi-Cation interactions: A:K.66

12 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: A.49, P.50 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: V.231, E.232 Chain B: Q.9 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: R.6, M.98 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: R.44 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: T.178 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: P.20, L.78 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: Y.85, D.137, M.138, A.139 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: E.173, Q.180 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain B: N.43, G.44, A.80 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain B: S.53, Y.68 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain B: E.51, H.52 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Ligands: TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU.1, TYR-LEU-GLN-LEU-ARG-THR-PHE-LEU-LEU.1 Ligand excluded by PLIP

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

PEG.10: 3 residues within 4Å: Chain A: T.80, G.83, Y.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.83, A:Y.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dolton, G. et al., Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell (2022)

Release Date

2021-07-28

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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