SMTL ID : 6jp3.1

Crystal structure of peptide in complex with HLA-A1101.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

hetero-1-1-mer

Ligands

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

ALA-THR-ILE-GLY-THR.1: 13 residues within 4Å: Chain A: M.5, Y.7, Y.9, M.45, Q.62, E.63, N.66, Y.99, Q.156, Y.159, R.163, W.167, Y.171 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.99, A:Y.159, A:Y.159, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Q.62, A:E.63, A:N.66, A:N.66, A:Y.99, A:R.163, A:Y.171, A:Y.171 Water bridges: A:R.65, A:Y.99, A:R.163

1 x ALA- MET- TYR- LYS: ALA-MET-TYR-LYS(Non-covalent)

ALA-MET-TYR-LYS.2: 14 residues within 4Å: Chain A: T.73, V.76, D.77, T.80, L.81, Y.84, I.95, D.116, T.143, K.146, W.147, A.152, Q.156 Ligands: GOL.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.73, A:V.76, A:L.81, A:T.143, A:W.147 Hydrogen bonds: A:T.73, A:D.77, A:Y.84, A:D.116, A:D.116, A:Q.155 Water bridges: A:D.77, A:D.77 Salt bridges: A:K.146

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.63 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.30, A:D.30, B:Y.63, B:Y.63 GOL.4: 3 residues within 4Å: Chain A: H.191, H.192, P.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.192 Water bridges: A:H.192 GOL.5: 4 residues within 4Å: Chain A: Q.70, I.97, R.114 Ligands: ALA-MET-TYR-LYS.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.70, A:D.77, A:R.114, A:R.114 Water bridges: A:T.73, A:D.74 GOL.6: 10 residues within 4Å: Chain A: H.188, W.204, L.206, R.234, Q.242 Chain B: Y.10, S.11, H.13, P.14, R.97 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.11, B:S.11, B:R.97, A:H.188, A:R.234, A:Q.242 Water bridges: B:S.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huan, X. et al., Crystal structure of suboptimal viral fragments of Epstein Barr Virus Rta peptide-HLA complex that stimulate CD8 T cell response. Sci Rep (2019)

Release Date

2020-01-29

Peptides

HLA class I histocompatibility antigen, A-11 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-11 alpha chain

Beta-2-microglobulin

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