SMTL ID : 8pje.1 (1 other biounit)

Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus haemagglutinin (HA)306-318 PKYVKQNTLKLAT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 6 residues within 4Å: Chain A: P.100, V.101, E.102, F.184, D.185 Chain B: Y.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.101, A:D.185 Salt bridges: A:E.102, A:E.102

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

EDO.2: 3 residues within 4Å: Chain A: K.79, R.80, N.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.79, A:K.79, A:R.80, A:N.82 EDO.3: 3 residues within 4Å: Chain A: V.89, P.90, K.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.115 EDO.4: 4 residues within 4Å: Chain A: R.104, S.160, T.161, E.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.104, A:T.161, A:T.161 EDO.5: 2 residues within 4Å: Chain A: N.82, T.84 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: W.172, G.173, L.174, D.175 Chain B: G.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.2, B:G.2, A:G.173, A:D.175 EDO.9: 6 residues within 4Å: Chain B: E.180, H.181, V.184, T.185, S.186, P.187 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.180, B:H.181, B:H.181 EDO.10: 4 residues within 4Å: Chain B: P.101, K.102, V.103, V.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.103 EDO.11: 5 residues within 4Å: Chain B: S.130, E.132, E.180, H.181, P.182 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.132, B:E.132 EDO.12: 3 residues within 4Å: Chain A: F.55 Chain B: S.92, F.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.92 EDO.13: 3 residues within 4Å: Chain B: A.62, E.63, N.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.66 Water bridges: B:E.50 EDO.14: 3 residues within 4Å: Chain B: R.134, E.141, K.143 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.134, B:K.143 EDO.20: 4 residues within 4Å: Chain A: F.58 Chain C: Y.3, V.4, K.5 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.5 Water bridges: C:Y.3, A:E.59, A:G.62 EDO.21: 4 residues within 4Å: Chain B: Y.64, Q.68 Chain C: L.9, K.10 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.10, B:Y.64, B:Y.64, B:Q.68 Water bridges: C:T.8

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: G.53, R.54, A.56, S.57 Chain C: P.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.56, C:P.1 GOL.8: 6 residues within 4Å: Chain A: R.48, S.137, E.138, T.139, Y.154 Ligands: GOL.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.48, A:S.137 Water bridges: A:E.138 GOL.15: 2 residues within 4Å: Chain B: W.192, R.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.193, B:R.193 GOL.16: 5 residues within 4Å: Chain B: E.26, R.27, V.28, V.79, R.84 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.26, B:V.28, B:R.84, B:R.84 Water bridges: B:V.28 GOL.17: 6 residues within 4Å: Chain A: R.48, N.98, V.108, Y.154 Chain B: D.156 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.48, A:R.48 GOL.18: 8 residues within 4Å: Chain B: I.131, E.132, V.133, S.148, G.150, L.151, T.161, V.163 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.133, B:S.148, B:T.161 Water bridges: B:L.151 GOL.19: 2 residues within 4Å: Chain B: E.56, R.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.56, B:R.59 GOL.22: 11 residues within 4Å: Chain A: N.73 Chain B: L.15, F.17, E.32, C.34, Y.51, W.65, R.75 Chain C: N.7, T.8, L.9 6 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Y.51, B:Y.51, B:R.75, C:L.9, A:N.73 Water bridges: B:W.13

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: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1 beta chain

Hemagglutinin

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