SMTL ID : 8pjg.1

F11 TCR in complex with Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A virus haemagglutinin (HA)306-318 PKYVKQNTLKLAR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain B: R.26, R.40, D.42, V.45, R.49 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.26, B:R.40 Water bridges: B:R.40, B:R.49 EDO.2: 6 residues within 4Å: Chain A: H.144 Chain B: Q.35, E.36, E.37, V.51, T.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.35, B:E.37 EDO.3: 7 residues within 4Å: Chain A: F.55, E.56, G.59 Chain C: V.4, K.5 Chain D: Q.97, D.98 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:D.98 Hydrogen bonds: C:K.5, C:K.5 EDO.4: 6 residues within 4Å: Chain D: L.8, V.12, L.21, L.22, R.23, T.107 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.21, D:R.23, D:T.107, D:T.107 EDO.5: 8 residues within 4Å: Chain B: Q.71, T.78 Chain D: P.31, P.32, Y.33, T.52, S.53, Q.97 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.71, B:T.78, D:P.32 Water bridges: B:T.78, D:Q.97 EDO.6: 6 residues within 4Å: Chain D: S.15, E.16, L.112, P.113, N.114, S.143 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.16 EDO.7: 7 residues within 4Å: Chain D: K.50, Y.51, T.52, S.53, A.54, A.55, V.58 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:T.52, D:S.53, D:A.54, D:A.55, D:A.55 Water bridges: B:D.67 EDO.8: 2 residues within 4Å: Chain D: N.192, I.194 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.192 EDO.10: 5 residues within 4Å: Chain E: L.114, N.115, E.219, W.220, T.221 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.115, E:T.221 Water bridges: E:D.113, E:L.114 EDO.11: 4 residues within 4Å: Chain E: P.8, R.9, N.10, Y.212 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.9, E:N.10, E:N.10, E:Y.212 EDO.12: 3 residues within 4Å: Chain E: V.163, H.164, S.165 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.164, E:S.165 Water bridges: E:S.165 EDO.13: 7 residues within 4Å: Chain E: E.126, P.127, E.129, I.132, W.198, R.239, D.241 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:E.126, E:E.129, E:R.239 Water bridges: D:R.126 EDO.14: 3 residues within 4Å: Chain E: R.36, R.44, N.84 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.44, E:R.44 EDO.15: 4 residues within 4Å: Chain E: Q.199, N.200, P.201, A.240 No protein-ligand interaction detected (PLIP) EDO.16: 6 residues within 4Å: Chain E: V.152, D.170, P.171, Q.172, P.173, L.187 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:V.152, E:D.170 Water bridges: E:R.107, E:V.152, D:N.42

2 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.9: 10 residues within 4Å: Chain D: K.133, S.134, Y.156, W.178, S.179, N.180 Chain E: F.125, L.143, T.145, E.176 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:E.176, D:Y.156 Water bridges: D:S.179 P4G.17: 3 residues within 4Å: Chain E: I.82, P.83, E.112 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.82, E:P.83, E:E.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hulin-Curtis, S. et al., A targeted single mutation in influenza A virus universal epitope transforms immunogenicity and protective immunity via CD4 + T cell activation. Cell Rep (2024)

Release Date

2024-06-19

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA class II histocompatibility antigen, DRB1 beta chain: B
Hemagglutinin HA2 chain: C
T cell receptor alpha chain constant: D
T cell receptor beta constant 1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1 beta chain

Hemagglutinin HA2 chain

T cell receptor alpha chain constant

T cell receptor beta constant 1

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