SMTL ID : 7wzz.1

Crystal structure of peptide KAGQVVTIW in complex with HLA-B5801

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

hetero-1-1-mer

Ligands

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

LYS-ALA-GLY-GLN-VAL-VAL-THR-ILE-TRP.1: 28 residues within 4Å: Chain A: M.5, Y.7, Y.9, Y.59, E.63, N.66, M.67, T.73, Y.74, E.76, N.77, I.80, Y.84, I.95, R.97, Y.99, A.117, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, W.167, Y.171 Ligands: GOL.2 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:Y.7, A:N.77, A:I.80, A:I.95, A:I.95, A:I.95, A:V.152, A:L.156, A:W.167 Hydrogen bonds: A:Y.7, A:Y.9, A:E.63, A:N.66, A:Y.74, A:Y.74, A:N.77, A:N.77, A:Y.84, A:Y.99, A:Y.99, A:K.146, A:Y.159, A:Y.171 Water bridges: A:G.62, A:N.66, A:R.97, A:R.97, A:R.97, A:R.97, A:R.97, A:W.147, A:Q.155 pi-Stacking: A:Y.123

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 12 residues within 4Å: Chain A: Y.74, R.97, D.114, Q.115, S.116, I.124, A.125, L.126, W.133, W.147, L.156 Ligands: LYS-ALA-GLY-GLN-VAL-VAL-THR-ILE-TRP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.114, A:D.114, A:D.114, A:S.116, A:L.126 GOL.3: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.63 3 PLIP interactions: 3 interactions with chain B Water bridges: B:F.56, B:Y.63, B:Y.63 GOL.4: 4 residues within 4Å: Chain A: N.127, E.128, D.129, S.132 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.127, A:E.128, A:D.129, A:D.129, A:S.132 Water bridges: A:N.127, A:E.128

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

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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