SMTL ID : 8pjf.1

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 1.48 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: K.115, R.144 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.114 Water bridges: A:R.144 Salt bridges: A:K.115, A:R.144 SO4.2: 3 residues within 4Å: Chain A: R.127, N.128, K.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.128 Water bridges: A:R.127, A:R.127 Salt bridges: A:R.127, A:K.130 SO4.8: 3 residues within 4Å: Chain B: R.29, L.31, R.43 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.29, B:R.43 SO4.9: 5 residues within 4Å: Chain B: A.53, V.54, T.55, E.56, R.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.54 Salt bridges: B:R.59 SO4.21: 6 residues within 4Å: Chain A: A.65, N.66, V.69 Chain C: K.5, N.7, T.8 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.66, C:T.8 Salt bridges: C:K.5 SO4.22: 3 residues within 4Å: Chain B: H.85 Chain C: P.1, K.2 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.2 Salt bridges: B:H.85

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

EDO.3: 6 residues within 4Å: Chain A: G.53, R.54, F.55, A.56, S.57 Chain C: P.1 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: T.97, S.99, P.100 Chain B: Y.106, S.122, Q.160, L.162 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: P.100, V.101, E.102 Chain B: Y.106 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: R.144, E.145, D.146 Ligands: SO4.1 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: T.45, W.47, S.57, F.58 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: E.26, R.27, V.28, V.79, R.84 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain B: I.131, V.133, S.148, G.150, L.151, T.161, V.163 Ligands: EDO.19 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: N.138, R.170, G.172, E.173 Ligands: EDO.15 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: P.101, K.102, V.103, V.190 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: E.191, W.192, R.193 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: R.137, N.138, Q.140, E.173 Ligands: EDO.12 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: Q.111, L.113, H.116, N.117 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: L.118, G.145, V.147, L.165, E.166 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: E.8, H.9 Chain B: V.95, R.98 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: G.150, L.151 Ligands: EDO.11 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: N.98, S.99 Chain B: K.102, S.124, G.125 Ligand excluded by PLIP

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

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 HA2 chain

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