SMTL ID : 6tzb.1

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in complex with 6'-SLNLN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.30, A.31, T.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: N.157, T.159 Chain C: S.211, P.213, W.214 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:W.214 Hydrophobic interactions: A:T.159 NAG-NAG-BMA.6: 5 residues within 4Å: Chain C: S.37, N.277, V.289, N.290 Chain D: E.69 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 5 residues within 4Å: Chain A: S.37, N.277, V.289, N.290, K.291 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain E: N.30, T.32, T.310 Chain F: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: S.37, N.277, V.289, N.290 Chain F: E.69 No protein-ligand interaction detected (PLIP)

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

NAG-GAL-NAG-GAL-SIA.4: 12 residues within 4Å: Chain A: Y.90, G.127, S.128, N.129, W.145, K.148, H.175, E.182, S.185, L.186, L.218, S.220 7 PLIP interactions: 7 interactions with chain A Water bridges: A:S.178, A:S.178 Hydrophobic interactions: A:W.145 Hydrogen bonds: A:G.127, A:N.129, A:N.129, A:A.130, A:H.175, A:S.220 NAG-GAL-NAG-GAL-SIA.11: 15 residues within 4Å: Chain E: Y.90, G.126, G.127, S.128, N.129, W.145, T.147, K.148, G.150, H.175, E.182, S.185, L.186, L.218, S.220 11 PLIP interactions: 11 interactions with chain E Water bridges: E:S.178, E:G.127, E:G.127, E:S.137, E:S.220 Hydrophobic interactions: E:T.147 Hydrogen bonds: E:Y.90, E:G.127, E:N.129, E:N.129, E:E.182, E:S.220

1 x NAG- NAG- BMA- MAN: 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.5: 7 residues within 4Å: Chain C: N.157, T.159, R.199 Chain E: S.211, R.212, P.213, W.214 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:W.214, C:R.199

1 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.7: 12 residues within 4Å: Chain C: Y.90, G.126, G.127, S.128, N.129, W.145, H.175, E.182, L.186, W.214, L.218, S.220 7 PLIP interactions: 7 interactions with chain C Water bridges: C:S.178, C:S.220 Hydrogen bonds: C:Y.90, C:G.127, C:N.129, C:N.129, C:H.175, C:S.220

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.9: 6 residues within 4Å: Chain A: S.211, P.213, W.214 Chain E: N.157, T.159, V.234 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:V.234 Hydrogen bonds: A:W.214

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

NAG.12: 4 residues within 4Å: Chain A: Q.72, N.73, E.111, F.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.73, A:E.111 Water bridges: A:Q.72, A:N.73 NAG.13: 1 residues within 4Å: Chain C: N.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.30 Water bridges: C:T.310 NAG.14: 4 residues within 4Å: Chain C: Q.72, N.73, E.111, F.112 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.73 Water bridges: C:Q.72, C:R.142 NAG.15: 5 residues within 4Å: Chain D: A.147, E.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.147 NAG.16: 3 residues within 4Å: Chain E: D.69, V.70, N.73 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, N.C. et al., Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape. Nat Commun (2020)

Release Date

2019-10-30

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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