SMTL ID : 4nrk.1

Structure of hemagglutinin with F95Y mutation of influenza virus B/Lee/40 complex with LSTc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: S.12, P.13, V.15, N.25, Y.336 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.145, T.147, G.149, N.150 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: E.291, N.303 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: I.30, N.332 Chain B: W.21, Q.42, I.45, T.49 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.42 NAG-NAG.6: 5 residues within 4Å: Chain C: S.12, P.13, V.15, N.25, Y.336 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: E.291, G.301, N.303 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: I.30, N.332 Chain D: W.21, I.45 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain E: S.12, P.13, V.15, N.25, Y.336 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: N.145, T.147, G.149, N.150 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain E: F.230, N.232 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain E: E.291, G.301, N.303 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain E: I.30, N.332 Chain F: W.21 No protein-ligand interaction detected (PLIP)

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

NAG-GAL-SIA.5: 17 residues within 4Å: Chain A: Y.95, G.138, T.139, S.140, G.141, N.150, W.158, I.160, D.195, Q.199, R.202, L.203, L.239, K.240, Q.241, S.242, G.243 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.240, A:T.139, A:G.141, A:D.195, A:Q.199, A:R.202, A:Q.241, A:Q.241, A:G.243 Hydrophobic interactions: A:L.203 Water bridges: A:T.139, A:N.150 NAG-GAL-SIA.10: 13 residues within 4Å: Chain C: Y.95, T.139, S.140, G.141, W.158, I.160, D.195, R.202, L.203, K.240, Q.241, S.242, G.243 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.240, C:T.139, C:G.141, C:D.195, C:R.202, C:Q.241, C:Q.241, C:S.242, C:G.243 Hydrophobic interactions: C:L.203 NAG-GAL-SIA.16: 17 residues within 4Å: Chain E: Y.95, G.138, T.139, S.140, G.141, N.150, W.158, I.160, D.195, Q.199, R.202, L.203, L.239, K.240, Q.241, S.242, G.243 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:K.240, E:K.240, E:Y.95, E:T.139, E:G.141, E:N.150, E:D.195, E:Q.199, E:R.202, E:Q.241, E:Q.241, E:G.243 Water bridges: E:N.150, E:T.139, E:T.139 Hydrophobic interactions: E:L.203

1 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(Post Translational Modification)

NAG-NAG-BMA.7: 4 residues within 4Å: Chain C: N.145, T.147, G.149, N.150 No protein-ligand interaction detected (PLIP)

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

NAG.17: 1 residues within 4Å: Chain A: N.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.232 NAG.18: 1 residues within 4Å: Chain B: N.145 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.145 NAG.19: 1 residues within 4Å: Chain C: N.232 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain D: N.145, T.147 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.145, D:T.147 NAG.21: 3 residues within 4Å: Chain E: N.59, R.69, E.237 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.59 NAG.22: 2 residues within 4Å: Chain F: N.145, T.147 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.145, F:T.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, F. et al., The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Virology (2014)

Release Date

2014-03-12

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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