SMTL ID : 5f9j.1

Structure of HLA-A2:01 with peptide Y9L

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TYR- LEU- SER- PRO- ILE- ALA- SER- PRO- LEU: Peptide Y9L(Non-covalent)

TYR-LEU-SER-PRO-ILE-ALA-SER-PRO-LEU.1: 24 residues within 4Å: Chain A: M.5, Y.7, F.9, M.45, E.63, K.66, V.67, H.70, T.73, D.77, L.81, Y.84, Y.99, Y.123, T.143, K.146, W.147, V.152, Q.155, Y.159, T.163, W.167, Y.171 Ligands: GOL.4 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Y.7, A:F.9, A:V.67, A:L.81, A:Y.123, A:T.143, A:W.147, A:T.163, A:W.167, A:W.167 Hydrogen bonds: A:E.63, A:K.66, A:D.77, A:Y.84, A:Y.84, A:Y.99, A:Y.99, A:K.146, A:Q.155, A:Y.159, A:Y.171 Water bridges: A:Y.7, A:D.77, A:R.97 Salt bridges: A:K.146 pi-Stacking: A:W.167 pi-Cation interactions: A:K.66

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.6, Y.27, D.29, D.30 Chain B: Y.63 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.6, A:D.30, B:Y.63 GOL.3: 10 residues within 4Å: Chain A: W.204, R.234, W.244 Chain B: V.9, Y.10, S.11, W.95, D.96, R.97, D.98 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.234, A:W.244, B:V.9, B:S.11, B:S.11 GOL.4: 10 residues within 4Å: Chain A: R.97, H.114, W.147, V.152, Q.155, L.156 Ligands: TYR-LEU-SER-PRO-ILE-ALA-SER-PRO-LEU.1, TYR-LEU-SER-PRO-ILE-ALA-SER-PRO-LEU.1, TYR-LEU-SER-PRO-ILE-ALA-SER-PRO-LEU.1, TYR-LEU-SER-PRO-ILE-ALA-SER-PRO-LEU.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.97, A:R.97, A:Q.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Remesh, S.G. et al., Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT. J. Biol. Chem. (2017)

Release Date

2016-12-21

Peptides

HLA class I histocompatibility antigen, A-2 alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HLA class I histocompatibility antigen, A-2 alpha chain

Beta-2-microglobulin

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