SMTL ID : 8tj6.3 (3 other biounits)

CRYSTAL STRUCTURE OF THE A/Beijing/353/1989(H3N2) INFLUENZA VIRUS HEMAGGLUTININ WITH HUMAN RECEPTOR ANALOG 6'-SLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 8 residues within 4Å: Chain A: N.32, T.34, T.312 Chain B: W.21, I.45, I.48, N.49, L.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.312 NAG-NAG-FUC.8: 8 residues within 4Å: Chain C: N.32, T.34, T.312 Chain D: W.21, I.45, I.48, N.49, L.52 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.312 NAG-NAG-FUC.15: 8 residues within 4Å: Chain E: N.32, T.34, T.312 Chain F: W.21, I.45, I.48, N.49, L.52 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.312

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 6 residues within 4Å: Chain A: N.159, T.161 Chain E: S.213, R.214, P.215, W.216 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:W.216 NAG-NAG-BMA-MAN-MAN.9: 6 residues within 4Å: Chain A: S.213, R.214, P.215, W.216 Chain C: N.159, T.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.216 NAG-NAG-BMA-MAN-MAN.16: 6 residues within 4Å: Chain C: S.213, R.214, P.215, W.216 Chain E: N.159, T.161 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.216

3 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.3: 11 residues within 4Å: Chain A: Y.92, E.129, S.130, Y.131, W.147, H.177, E.184, L.188, G.219, L.220, S.222 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.219, A:Y.92, A:E.129, A:Y.131, A:H.177, A:S.222 Hydrophobic interactions: A:Y.131, A:L.188 NAG-GAL-SIA.10: 11 residues within 4Å: Chain C: Y.92, E.129, S.130, Y.131, W.147, H.177, E.184, L.188, G.219, L.220, S.222 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.219, C:Y.92, C:E.129, C:Y.131, C:H.177, C:S.222 Hydrophobic interactions: C:Y.131, C:L.188 NAG-GAL-SIA.17: 11 residues within 4Å: Chain E: Y.92, E.129, S.130, Y.131, W.147, H.177, E.184, L.188, G.219, L.220, S.222 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:G.219, E:Y.92, E:E.129, E:Y.131, E:H.177, E:S.222 Hydrophobic interactions: E:Y.131, E:L.188

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 3 residues within 4Å: Chain A: S.39, N.279, V.291 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.291 Hydrogen bonds: A:N.279, A:V.291 NAG.5: 2 residues within 4Å: Chain A: K.56, N.57 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.56 Hydrogen bonds: A:N.57 NAG.6: 2 residues within 4Å: Chain A: N.120, T.122 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain B: A.147, G.150, N.154 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain C: S.39, N.279, V.291 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.291 Hydrogen bonds: C:N.279, C:V.291 NAG.12: 2 residues within 4Å: Chain C: K.56, N.57 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.56 Hydrogen bonds: C:N.57 NAG.13: 2 residues within 4Å: Chain C: N.120, T.122 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain D: A.147, G.150, N.154 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain E: S.39, N.279, V.291 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.291 Hydrogen bonds: E:N.279, E:V.291 NAG.19: 2 residues within 4Å: Chain E: K.56, N.57 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.56 Hydrogen bonds: E:N.57 NAG.20: 2 residues within 4Å: Chain E: N.120, T.122 No protein-ligand interaction detected (PLIP) NAG.21: 3 residues within 4Å: Chain F: A.147, G.150, N.154 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.J. et al., Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site. Cell Host Microbe (2024)

Release Date

2024-02-14

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
E

E
E

B
F

D
F

F
F

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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