SMTL ID : 7r7y.1

Crystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived epitope QW9 S3T variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLN- ALA- THR- GLN- GLU- VAL- LYS- ASN- TRP: GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP(Non-covalent)

GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP.1: 24 residues within 4Å: Chain A: Y.7, Y.9, E.63, N.66, M.67, S.70, T.73, Y.74, E.76, N.77, I.80, Y.84, I.95, Y.99, A.117, Y.123, T.143, K.146, W.147, V.152, Q.155, Y.159, W.167, Y.171 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:T.73, A:Y.74, A:N.77, A:I.80, A:I.95, A:I.95, A:I.95, A:Y.99, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Y.9, A:E.63, A:E.63, A:N.66, A:Y.74, A:E.76, A:E.76, A:N.77, A:Y.99, A:Y.99, A:T.143, A:Y.159, A:Y.171 Water bridges: A:Y.9, A:E.63, A:N.66, A:S.70, A:S.70, A:N.77, A:S.116 Salt bridges: A:K.146 pi-Stacking: A:Y.123

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.63 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.30, B:Y.63 GOL.3: 2 residues within 4Å: Chain A: S.251, E.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.251, A:E.253 GOL.4: 4 residues within 4Å: Chain A: L.163, E.166, W.167, R.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.166 Water bridges: A:R.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide. Nat Commun (2023)

Release Date

2022-06-29

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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