SMTL ID : 7x1b.1

Crystal structure of peptide KAGQVVTI in complex with HLA-B5801

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LYS- ALA- GLY- GLN- VAL- VAL- THR- ILE: LYS-ALA-GLY-GLN-VAL-VAL-THR-ILE(Non-covalent)

LYS-ALA-GLY-GLN-VAL-VAL-THR-ILE.1: 22 residues within 4Å: Chain A: M.5, Y.7, Y.9, Y.59, E.63, N.66, M.67, S.70, T.73, Y.74, N.77, I.80, Y.84, R.97, Y.99, T.143, K.146, W.147, Y.159, W.167, Y.171 Ligands: GOL.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.9, A:T.73, A:I.80, A:W.147, A:W.167 Hydrogen bonds: A:Y.7, A:Y.7, A:E.63, A:N.66, A:N.77, A:N.77, A:R.97, A:R.97, A:Y.99, A:Y.99, A:T.143, A:Y.159 Water bridges: A:Y.9, A:Y.9, A:T.73 Salt bridges: A:K.146

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30 Chain B: F.56, Y.63 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.63, A:D.29 GOL.3: 9 residues within 4Å: Chain A: Y.74, N.77, R.97, D.114, S.116, W.147 Ligands: LYS-ALA-GLY-GLN-VAL-VAL-THR-ILE.1, LYS-ALA-GLY-GLN-VAL-VAL-THR-ILE.1, LYS-ALA-GLY-GLN-VAL-VAL-THR-ILE.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.74, A:Y.74, A:N.77, A:S.116 Water bridges: A:R.97, A:R.97, A:R.97, A:D.114, A:D.114 GOL.4: 5 residues within 4Å: Chain A: L.82, R.83, N.86, Q.87, S.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.82, A:N.86, A:Q.87 Water bridges: A:E.89

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

Related Entries With Identical Sequence