SMTL ID : 7l1c.1

Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ALA- LEU- HIS- GLY- GLY- TRP- THR- THR- LYS: mutant PIK3CA peptide(Non-covalent)

ALA-LEU-HIS-GLY-GLY-TRP-THR-THR-LYS.1: 28 residues within 4Å: Chain A: M.5, Y.7, F.9, M.45, E.63, N.66, V.67, A.69, Q.70, T.73, V.76, D.77, T.80, L.81, Y.84, I.95, Y.99, D.116, T.143, K.146, W.147, A.150, E.152, Q.155, L.156, Y.159, W.167, Y.171 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Y.7, A:F.9, A:V.67, A:A.69, A:T.73, A:V.76, A:L.81, A:T.143, A:W.147, A:A.150, A:Y.159, A:W.167 Hydrogen bonds: A:E.63, A:D.77, A:Y.99, A:Y.99, A:D.116, A:T.143, A:K.146, A:E.152, A:Y.171, A:Y.171 Water bridges: A:N.66, A:Q.70, A:D.77, A:E.152 Salt bridges: A:K.146

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Y.85, Q.87, Y.118, D.119 Chain B: I.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.87, A:D.119 GOL.3: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.64 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.64, B:Y.64, A:R.6 Water bridges: A:R.6, A:D.29 GOL.6: 7 residues within 4Å: Chain B: I.8, Q.9, V.10, V.94, K.95, W.96, D.97 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.10, B:K.95, B:D.97 Water bridges: A:R.234 GOL.7: 5 residues within 4Å: Chain A: R.21, I.23 Chain B: S.34, D.35, L.55 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.34, B:D.35 Water bridges: B:H.52 GOL.8: 8 residues within 4Å: Chain A: W.204, R.234, Q.242 Chain B: Y.11, S.12, R.13, H.14, P.15 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.12, A:R.234, A:Q.242, A:Q.242 Water bridges: B:S.12, B:R.98

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 5 residues within 4Å: Chain A: S.13, L.78, G.79, R.82, H.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.13 FMT.5: 3 residues within 4Å: Chain A: P.57, E.58, D.61 No protein-ligand interaction detected (PLIP) FMT.9: 5 residues within 4Å: Chain B: D.35, I.36, E.37, N.84, H.85 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandran, S.S. et al., Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA. Nat Med (2022)

Release Date

2022-03-23

Peptides

HLA class I histocompatibility antigen, A 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 alpha chain

Beta-2-microglobulin

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