SMTL ID : 7sih.1

Crystal Structure of HLA B*3503 in complex with NPDIVIYQY, an 9-mer epitope from HIV-I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASN- PRO- ASP- ILE- VAL- TYR- GLN- TYR: Reverse transcriptase peptide NPDIVIYQY(Non-covalent)

ASN-PRO-ASP-ILE-VAL-TYR-GLN-TYR.1: 29 residues within 4Å: Chain A: M.5, Y.7, Y.9, Y.59, R.62, N.63, I.66, F.67, T.73, Y.74, E.76, S.77, N.80, L.81, Y.84, I.95, R.97, Y.99, F.116, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, W.167, Y.171 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:I.66, A:F.67, A:T.73, A:E.76, A:L.81, A:I.95, A:Y.123, A:T.143, A:W.147, A:V.152, A:V.152, A:L.156, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Y.9, A:R.62, A:R.62, A:N.63, A:E.76, A:S.77, A:Y.99, A:Y.99, A:Y.99, A:T.143, A:Q.155, A:Y.159, A:Y.171 Water bridges: A:R.97 Salt bridges: A:R.97, A:K.146

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: S.92, H.93, D.119 Chain B: I.1, Q.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.92, A:D.119, B:Q.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lobos, C.A. et al., Molecular insights into the HLA-B35 molecules' classification associated with HIV control. Immunol.Cell.Biol. (2024)

Release Date

2022-11-23

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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