SMTL ID : 4m44.1

Crystal structure of hemagglutinin of influenza virus B/Yamanashi/166/1998 in complex with avian-like receptor LSTa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-3-mer

Ligands

9 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: 2 residues within 4Å: Chain A: E.291, N.303 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: I.30, N.332 Chain B: W.21, I.45 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.45 NAG-NAG.5: 5 residues within 4Å: Chain C: S.12, P.13, V.15, N.25, Y.336 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: E.291, N.303 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.291 Hydrogen bonds: C:E.291 NAG-NAG.7: 4 residues within 4Å: Chain C: I.30, N.332 Chain D: W.21, I.45 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain E: S.12, P.13, V.15, N.25, Y.336 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain E: E.291, N.303 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain E: I.30, N.332 Chain F: W.21, I.45 No protein-ligand interaction detected (PLIP)

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

GAL-NAG-GAL-SIA.4: 12 residues within 4Å: Chain A: R.136, G.138, T.139, S.140, G.141, W.158, D.195, Q.199, L.203, P.240, Q.241, S.242 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.240, A:W.158 Water bridges: A:S.242, A:T.139, A:T.139, A:S.242, A:G.243 Hydrogen bonds: A:R.136, A:R.136, A:T.139, A:G.141, A:D.195, A:Q.241, A:Q.241 GAL-NAG-GAL-SIA.8: 13 residues within 4Å: Chain C: R.136, G.138, T.139, S.140, G.141, W.158, D.195, Q.199, L.203, L.239, P.240, Q.241, S.242 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:P.240, C:R.136, C:R.136, C:T.139, C:G.141, C:D.195, C:Q.241, C:Q.241 Water bridges: C:S.242, C:T.139, C:T.139, C:S.242, C:G.243 Hydrophobic interactions: C:W.158 GAL-NAG-GAL-SIA.12: 12 residues within 4Å: Chain E: R.136, G.138, T.139, S.140, G.141, W.158, D.195, Q.199, L.203, P.240, Q.241, S.242 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:P.240, E:R.136, E:R.136, E:T.139, E:G.141, E:D.195, E:Q.241, E:Q.241 Water bridges: E:S.242, E:S.242, E:T.139, E:T.139, E:T.139, E:S.242, E:S.242, E:G.243 Hydrophobic interactions: E:W.158

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

NAG.13: 3 residues within 4Å: Chain A: N.145, T.147, S.150 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.147 Hydrogen bonds: A:N.145, A:T.147 NAG.14: 2 residues within 4Å: Chain A: D.163, N.165 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.165 Hydrogen bonds: A:N.165 NAG.15: 3 residues within 4Å: Chain A: L.58, N.59, M.71 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain B: N.145, T.147 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.147, B:T.147 NAG.17: 3 residues within 4Å: Chain C: N.145, T.147, S.150 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.145, C:T.147 NAG.18: 2 residues within 4Å: Chain C: N.165, T.167 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.165, C:T.167, C:T.167 NAG.19: 1 residues within 4Å: Chain C: N.59 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain D: N.145, T.147 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.147 NAG.21: 4 residues within 4Å: Chain E: N.145, T.147, S.148, S.150 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.150 NAG.22: 2 residues within 4Å: Chain E: N.165, T.167 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.165, E:N.165 NAG.23: 2 residues within 4Å: Chain E: L.58, N.59 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.59 NAG.24: 2 residues within 4Å: Chain F: N.145, T.147 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.147, F:T.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, F. et al., Structural basis for the divergent evolution of influenza B virus hemagglutinin. Virology (2013)

Release Date

2013-09-25

Peptides

Hemagglutinin HA1: ACE
Hemagglutinin HA2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin HA1

Hemagglutinin HA2

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