SMTL ID : 6nsa.1

Crystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin in complex with 3'-SLNLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-3-3-mer

Ligands

6 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.5: 9 residues within 4Å: Chain A: A.155, L.156, N.157, R.193, N.238, S.239, T.240 Chain E: I.209 Ligands: NAG-NAG-BMA-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.10: 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.14: 9 residues within 4Å: Chain A: I.209 Chain C: A.155, L.156, N.157, R.193, N.238, S.239, T.240 Ligands: NAG-NAG-BMA-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.19: 4 residues within 4Å: Chain E: N.30, T.32, T.310 Chain F: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 9 residues within 4Å: Chain C: I.209 Chain E: A.155, L.156, N.157, R.193, N.238, S.239, T.240 Ligands: NAG-NAG-BMA-MAN-MAN.21 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.11: 3 residues within 4Å: Chain C: E.54, N.55, Y.86 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.37, N.277, V.289, N.290 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain E: E.54, N.55, Y.86 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 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- 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.3: 11 residues within 4Å: Chain A: N.157, T.159, I.234, L.236 Chain E: Y.211, P.213, R.214, N.217 Ligands: NAG-NAG-BMA-MAN.5, NAG-NAG-BMA-MAN.5, GAL-NAG-GAL-SIA.24 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.214, E:R.214, E:R.214 Hydrophobic interactions: A:I.234 NAG-NAG-BMA-MAN-MAN.12: 11 residues within 4Å: Chain A: Y.211, P.213, R.214, N.217 Chain C: N.157, T.159, I.234, L.236 Ligands: GAL-NAG-GAL-SIA.6, NAG-NAG-BMA-MAN.14, NAG-NAG-BMA-MAN.14 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.214, A:R.214, A:R.214 Hydrophobic interactions: C:I.234 NAG-NAG-BMA-MAN-MAN.21: 11 residues within 4Å: Chain C: Y.211, P.213, R.214, N.217 Chain E: N.157, T.159, I.234, L.236 Ligands: GAL-NAG-GAL-SIA.15, NAG-NAG-BMA-MAN.23, NAG-NAG-BMA-MAN.23 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:R.214, C:R.214, C:R.214 Hydrophobic interactions: E:I.234

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

GAL-NAG-GAL-SIA.6: 16 residues within 4Å: Chain A: Y.90, G.126, T.127, S.128, S.129, N.137, W.145, T.147, H.175, K.181, D.182, L.186, N.217, I.218, S.220 Ligands: NAG-NAG-BMA-MAN-MAN.12 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.181, A:D.182, A:N.217, A:Y.90, A:T.127, A:S.129, A:H.175, A:D.182, A:S.220 Water bridges: A:R.214, A:S.129, A:R.214, A:T.127, A:T.127 Hydrophobic interactions: A:W.145, A:T.147 GAL-NAG-GAL-SIA.15: 16 residues within 4Å: Chain C: Y.90, G.126, T.127, S.128, S.129, N.137, W.145, T.147, H.175, K.181, D.182, L.186, N.217, I.218, S.220 Ligands: NAG-NAG-BMA-MAN-MAN.21 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.181, C:D.182, C:N.217, C:Y.90, C:T.127, C:S.129, C:H.175, C:D.182, C:S.220 Water bridges: C:R.214, C:S.129, C:R.214, C:T.127, C:T.127 Hydrophobic interactions: C:W.145, C:T.147 GAL-NAG-GAL-SIA.24: 16 residues within 4Å: Chain E: Y.90, G.126, T.127, S.128, S.129, N.137, W.145, T.147, H.175, K.181, D.182, L.186, N.217, I.218, S.220 Ligands: NAG-NAG-BMA-MAN-MAN.3 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:K.181, E:D.182, E:N.217, E:Y.90, E:T.127, E:S.129, E:H.175, E:D.182, E:S.220 Water bridges: E:R.214, E:S.129, E:R.214, E:T.127, E:T.127 Hydrophobic interactions: E:W.145, E:T.147

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

NAG.7: 4 residues within 4Å: Chain A: N.14, T.16, T.29, N.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.14 Water bridges: A:N.30 NAG.8: 2 residues within 4Å: Chain A: Q.124, N.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG.9: 4 residues within 4Å: Chain B: A.147, S.151, N.154, T.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.154, B:T.156 NAG.16: 4 residues within 4Å: Chain C: N.14, T.16, T.29, N.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.14 Water bridges: C:N.30 NAG.17: 2 residues within 4Å: Chain C: Q.124, N.125 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.125 NAG.18: 4 residues within 4Å: Chain D: A.147, S.151, N.154, T.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.154, D:T.156 NAG.25: 4 residues within 4Å: Chain E: N.14, T.16, T.29, N.30 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.14 Water bridges: E:N.30 NAG.26: 2 residues within 4Å: Chain E: Q.124, N.125 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.125 NAG.27: 4 residues within 4Å: Chain F: A.147, S.151, N.154, T.156 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.154, 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

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