SMTL ID : 7rrg.1

Crystal structure of human 0606T1-2 TCR bound to HLA-A*03:01 in complex with a mutant PIK3CA peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-1-1-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: 34 residues within 4Å: Chain A: Y.7, F.9, M.45, Q.62, E.63, N.66, V.67, T.73, V.76, D.77, T.80, L.81, Y.84, I.95, I.97, Y.99, R.114, D.116, W.133, T.143, K.146, W.147, E.152, A.153, Q.155, L.156, Y.159, W.167, Y.171 Chain C: Y.33, A.94 Chain D: T.101, Y.102 Ligands: GOL.12 40 PLIP interactions: 36 interactions with chain A, 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:Y.7, A:F.9, A:N.66, A:V.67, A:V.76, A:D.77, A:Y.99, A:W.133, A:T.143, A:W.147, A:E.152, A:L.156, A:Y.159, A:W.167 Hydrogen bonds: A:E.63, A:D.77, A:Y.99, A:Y.99, A:R.114, A:R.114, A:D.116, A:T.143, A:K.146, A:K.146, A:Q.155, A:Y.159, A:Y.171, C:Y.33, D:Y.102 Water bridges: A:Q.62, A:N.66, A:N.66, A:Y.84, A:E.152, A:Q.155, C:A.94, C:A.94 Salt bridges: A:K.146 pi-Stacking: A:W.147, A:W.147

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.64, A:D.30 GOL.3: 5 residues within 4Å: Chain A: A.135, A.136, D.137, M.138, Q.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.135, A:Q.141, A:Q.141 GOL.4: 4 residues within 4Å: Chain A: A.149, A.150, H.151 Chain C: V.56 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:T.57, A:E.152 GOL.5: 4 residues within 4Å: Chain A: G.18, E.19, P.20, R.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.19, A:R.75 Water bridges: A:R.14 GOL.6: 10 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.11, S.12, H.14, P.15, R.98, M.100 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.234, A:Q.242, B:S.12, B:H.14 Water bridges: A:W.204 GOL.7: 6 residues within 4Å: Chain B: D.77, E.78, Y.79, W.96, R.98 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.79, B:Y.79, B:W.96, B:R.98 GOL.8: 5 residues within 4Å: Chain B: E.78, Y.79, K.95, W.96 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.78, B:Y.79, B:Y.79, B:K.95, B:W.96 GOL.9: 4 residues within 4Å: Chain A: R.21 Chain B: S.34, D.35, L.65 3 PLIP interactions: 3 interactions with chain B Water bridges: B:I.36, B:H.52, B:S.53 GOL.10: 5 residues within 4Å: Chain B: Q.3, V.86, T.87, L.88, S.89 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.89 GOL.11: 4 residues within 4Å: Chain B: P.6, K.7, I.8, K.92 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.6, B:I.8, B:K.92, B:K.92 GOL.12: 5 residues within 4Å: Chain A: K.146 Chain D: L.97, Y.102 Ligands: ALA-LEU-HIS-GLY-GLY-TRP-THR-THR-LYS.1, ALA-LEU-HIS-GLY-GLY-TRP-THR-THR-LYS.1 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Y.102, D:Y.102, A:K.146 Water bridges: A:K.146 GOL.13: 9 residues within 4Å: Chain C: Y.33, T.35, Q.50, L.90, V.91, G.92, G.93 Chain D: E.100, T.101 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.33, C:T.35, C:Q.50, C:G.92, C:G.92 Water bridges: D:E.100, D:Y.102 GOL.14: 5 residues within 4Å: Chain C: F.47, I.48, N.58, V.60 Chain D: E.103 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.48, C:N.58

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
T cell receptor, alpha chain: C
T cell receptor, beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

HLA class I histocompatibility antigen, A alpha chain

Beta-2-microglobulin

T cell receptor, alpha chain

T cell receptor, beta chain

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