SMTL ID : 6ns9.1

Crystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-3-3-mer

Ligands

3 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.1: 4 residues within 4Å: Chain A: N.30, T.32, T.310 Chain B: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.9: 4 residues within 4Å: Chain C: N.30, T.32, T.310 Chain D: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.17: 4 residues within 4Å: Chain E: N.30, T.32, T.310 Chain F: L.52 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain A: E.54, N.55, Y.86 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.37, N.277, V.289, N.290 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: E.54, N.55, Y.86 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.37, N.277, V.289, N.290 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain E: E.54, N.55, Y.86 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: N.37, N.277, V.289, N.290 No protein-ligand interaction detected (PLIP)

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.3: 6 residues within 4Å: Chain A: N.157, T.159 Chain E: Y.211, P.213, R.214, N.217 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.214, E:R.214 Water bridges: E:R.214 NAG-NAG-BMA.11: 6 residues within 4Å: Chain A: Y.211, P.213, R.214, N.217 Chain C: N.157, T.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.214, A:R.214 Water bridges: A:R.214 NAG-NAG-BMA.19: 6 residues within 4Å: Chain C: Y.211, P.213, R.214, N.217 Chain E: N.157, T.159 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.214, C:R.214 Water bridges: C:R.214

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

NAG.5: 2 residues within 4Å: Chain A: N.14, N.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.14 Water bridges: A:N.30 NAG.6: 1 residues within 4Å: Chain A: N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG.7: 8 residues within 4Å: Chain A: A.155, L.156, N.157, R.193, T.195, N.238, T.240 Chain E: I.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.238 NAG.8: 4 residues within 4Å: Chain B: A.147, G.150, S.151, N.154 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.147 Hydrogen bonds: B:N.154 Water bridges: B:T.156 NAG.13: 2 residues within 4Å: Chain C: N.14, N.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.14 Water bridges: C:N.30 NAG.14: 1 residues within 4Å: Chain C: N.125 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.125 NAG.15: 8 residues within 4Å: Chain A: I.209 Chain C: A.155, L.156, N.157, R.193, T.195, N.238, T.240 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.238 NAG.16: 4 residues within 4Å: Chain D: A.147, G.150, S.151, N.154 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.147 Hydrogen bonds: D:N.154 Water bridges: D:T.156 NAG.21: 2 residues within 4Å: Chain E: N.14, N.30 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.14 Water bridges: E:N.30 NAG.22: 1 residues within 4Å: Chain E: N.125 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.125 NAG.23: 8 residues within 4Å: Chain C: I.209 Chain E: A.155, L.156, N.157, R.193, T.195, N.238, T.240 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.238 NAG.24: 4 residues within 4Å: Chain F: A.147, G.150, S.151, N.154 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:A.147 Hydrogen bonds: F:N.154 Water bridges: F:T.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, N.C. et al., Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Cell Host Microbe (2019)

Release Date

2019-04-24

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Related Entries With Identical Sequence