SMTL ID : 7x1c.1

Crystal structure of peptide VSFIEFVI in complex with HLA-B5801

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VAL- SER- PHE- ILE- GLU- PHE- VAL- ILE: VAL-SER-PHE-ILE-GLU-PHE-VAL-ILE(Non-covalent)

VAL-SER-PHE-ILE-GLU-PHE-VAL-ILE.1: 23 residues within 4Å: Chain A: M.5, Y.7, Y.9, Y.59, E.63, N.66, M.67, T.73, Y.74, N.77, I.80, Y.84, R.97, Y.99, 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:Y.74, A:N.77, A:I.80, A:I.80, A:Y.99, A:V.152, A:V.152, A:L.156, A:Y.159, A:Y.159, A:Y.159, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Y.9, A:E.63, A:N.66, A:Y.74, A:N.77, A:N.77, A:R.97, A:R.97, A:Y.99, A:Y.99, A:Y.159, A:Y.171 Water bridges: A:S.70, A:S.70, A:Y.74, A:W.147 Salt bridges: A:R.97

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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.29, A:D.29 Water bridges: A:D.30, B:Y.63 GOL.3: 10 residues within 4Å: Chain A: H.3, D.29, T.178, L.179, Q.180, R.181, A.182, Y.209, P.210, E.264 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.3, A:L.179, A:L.179, A:Q.180 Water bridges: A:G.1, A:A.182, A:Y.209 GOL.4: 7 residues within 4Å: Chain A: M.12, R.21, I.23 Chain B: S.33, D.34, L.54, L.64 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Water bridges: B:S.33, B:S.33, B:D.34, B:H.51, B:L.54, A:R.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huan, X. et al., Allopurinol non-covalently facilitates binding of unconventional peptides to HLA-B*58:01. Sci Rep (2023)

Release Date

2023-05-03

Peptides

HLA-B: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HLA-B

Beta-2-microglobulin

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