SMTL ID : 6bkt.3 (2 other biounits)

Crystal structure of the A/Michigan/15/2014 (H3N2) influenza virus hemagglutinin in complex with 6'-SLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: N.32, T.34, T.312 Chain B: L.52 Ligands: PEG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: N.159, T.161, I.236 Chain C: T.181, S.213, P.215, K.216 Ligands: NAG-NAG.4 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:P.215, A:I.236 Hydrogen bonds: C:K.216 NAG-NAG.3: 4 residues within 4Å: Chain A: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 10 residues within 4Å: Chain A: A.157, L.158, N.159, R.195, N.240, S.241, T.242 Chain C: K.183, I.211 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.183, C:K.183 NAG-NAG.16: 5 residues within 4Å: Chain C: N.32, T.34, T.312 Chain D: L.52 Ligands: PEG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 8 residues within 4Å: Chain C: N.159, T.161, I.236 Chain E: T.181, S.213, P.215, K.216 Ligands: NAG-NAG.19 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:P.215, C:I.236 Hydrogen bonds: E:K.216 NAG-NAG.18: 4 residues within 4Å: Chain C: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 10 residues within 4Å: Chain C: A.157, L.158, N.159, R.195, N.240, S.241, T.242 Chain E: K.183, I.211 Ligands: NAG-NAG.17 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.183, E:K.183 NAG-NAG.31: 5 residues within 4Å: Chain E: N.32, T.34, T.312 Chain F: L.52 Ligands: PEG.38 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 8 residues within 4Å: Chain A: T.181, S.213, P.215, K.216 Chain E: N.159, T.161, I.236 Ligands: NAG-NAG.34 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:P.215, E:I.236 Hydrogen bonds: A:K.216 NAG-NAG.33: 4 residues within 4Å: Chain E: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 10 residues within 4Å: Chain A: K.183, I.211 Chain E: A.157, L.158, N.159, R.195, N.240, S.241, T.242 Ligands: NAG-NAG.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.183, A:K.183

3 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.5: 14 residues within 4Å: Chain A: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, H.177, D.184, F.187, L.188, D.219, I.220, S.222 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.187, A:L.188, A:W.147, A:T.149 Water bridges: A:D.184, A:D.184, A:T.129, A:T.129 Hydrogen bonds: A:D.219, A:T.129, A:S.131, A:S.222 NAG-GAL-SIA.20: 14 residues within 4Å: Chain C: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, H.177, D.184, F.187, L.188, D.219, I.220, S.222 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.187, C:L.188, C:W.147, C:T.149 Water bridges: C:D.184, C:D.184, C:T.129, C:T.129 Hydrogen bonds: C:D.219, C:T.129, C:S.131, C:S.222 NAG-GAL-SIA.35: 14 residues within 4Å: Chain E: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, H.177, D.184, F.187, L.188, D.219, I.220, S.222 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.187, E:L.188, E:W.147, E:T.149 Water bridges: E:D.184, E:D.184, E:T.129, E:T.129 Hydrogen bonds: E:D.219, E:T.129, E:S.131, E:S.222

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

NAG.6: 3 residues within 4Å: Chain A: E.56, N.57, Y.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.57, A:Y.88 Water bridges: A:N.57 NAG.7: 2 residues within 4Å: Chain A: Q.126, N.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.127 Water bridges: A:R.249 NAG.11: 5 residues within 4Å: Chain B: A.147, G.150, S.151, N.154, T.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.154 Water bridges: B:A.147 NAG.21: 3 residues within 4Å: Chain C: E.56, N.57, Y.88 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.57, C:Y.88 Water bridges: C:N.57 NAG.22: 2 residues within 4Å: Chain C: Q.126, N.127 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.127 Water bridges: C:R.249 NAG.26: 5 residues within 4Å: Chain D: A.147, G.150, S.151, N.154, T.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.154 Water bridges: D:A.147 NAG.36: 3 residues within 4Å: Chain E: E.56, N.57, Y.88 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.57, E:Y.88 Water bridges: E:N.57 NAG.37: 2 residues within 4Å: Chain E: Q.126, N.127 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.127 Water bridges: E:R.249 NAG.41: 5 residues within 4Å: Chain F: A.147, G.150, S.151, N.154, T.156 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.154 Water bridges: F:A.147

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 7 residues within 4Å: Chain A: H.12, V.14, T.31, N.32, T.312 Chain B: W.21 Ligands: NAG-NAG.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.12, A:N.32, A:T.312, A:T.312 Water bridges: A:T.31, B:V.18 PEG.23: 7 residues within 4Å: Chain C: H.12, V.14, T.31, N.32, T.312 Chain D: W.21 Ligands: NAG-NAG.16 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.12, C:N.32, C:T.312, C:T.312 Water bridges: C:T.31, D:V.18 PEG.38: 7 residues within 4Å: Chain E: H.12, V.14, T.31, N.32, T.312 Chain F: W.21 Ligands: NAG-NAG.31 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:H.12, E:N.32, E:T.312, E:T.312 Water bridges: E:T.31, F:V.18

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 5 residues within 4Å: Chain A: S.118, F.119, N.120, W.121, Q.126 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.119, A:N.120, A:W.121, A:Q.126, A:Q.126 Water bridges: A:E.117 SO4.10: 3 residues within 4Å: Chain A: I.28, R.315 Chain B: A.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:G.1, B:G.1, A:R.315 Salt bridges: A:R.315 SO4.14: 4 residues within 4Å: Chain B: W.14, E.15, G.16, R.25 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:E.319, A:E.319 Hydrogen bonds: B:E.15, B:G.16 Salt bridges: B:R.25 SO4.15: 4 residues within 4Å: Chain B: R.127, H.159, N.160 Chain D: K.139 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.160, B:N.160, D:Y.141 Salt bridges: B:R.127, B:H.159 SO4.24: 5 residues within 4Å: Chain C: S.118, F.119, N.120, W.121, Q.126 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.119, C:N.120, C:W.121, C:Q.126, C:Q.126 Water bridges: C:E.117 SO4.25: 3 residues within 4Å: Chain C: I.28, R.315 Chain D: A.7 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:G.1, D:G.1, C:R.315 Salt bridges: C:R.315 SO4.29: 4 residues within 4Å: Chain D: W.14, E.15, G.16, R.25 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.15, D:G.16 Salt bridges: D:R.25 Water bridges: C:E.319, C:E.319 SO4.30: 4 residues within 4Å: Chain D: R.127, H.159, N.160 Chain F: K.139 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:N.160, D:N.160, F:Y.141 Salt bridges: D:R.127, D:H.159 SO4.39: 5 residues within 4Å: Chain E: S.118, F.119, N.120, W.121, Q.126 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:F.119, E:N.120, E:W.121, E:Q.126, E:Q.126 Water bridges: E:E.117 SO4.40: 3 residues within 4Å: Chain E: I.28, R.315 Chain F: A.7 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Water bridges: F:G.1, F:G.1, E:R.315 Salt bridges: E:R.315 SO4.44: 4 residues within 4Å: Chain F: W.14, E.15, G.16, R.25 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:E.15, F:G.16 Salt bridges: F:R.25 Water bridges: E:E.319, E:E.319 SO4.45: 4 residues within 4Å: Chain B: K.139 Chain F: R.127, H.159, N.160 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:N.160, F:N.160, B:Y.141 Salt bridges: F:R.127, F:H.159

6 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.12: 8 residues within 4Å: Chain A: F.288, R.301 Chain B: R.54, L.55, W.92 Chain D: Y.94, E.97, L.98 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: B:R.54, D:E.97, A:R.301 1PE.13: 3 residues within 4Å: Chain B: H.26, G.33, N.146 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.146 Water bridges: B:H.26, B:E.30, B:R.153 1PE.27: 8 residues within 4Å: Chain C: F.288, R.301 Chain D: R.54, L.55, W.92 Chain F: Y.94, E.97, L.98 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: C:R.301, F:E.97, D:R.54 1PE.28: 3 residues within 4Å: Chain D: H.26, G.33, N.146 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.146 Water bridges: D:H.26, D:E.30, D:R.153 1PE.42: 8 residues within 4Å: Chain B: Y.94, E.97, L.98 Chain E: F.288, R.301 Chain F: R.54, L.55, W.92 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: B:E.97, F:R.54, E:R.301 1PE.43: 3 residues within 4Å: Chain F: H.26, G.33, N.146 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.146 Water bridges: F:H.26, F:E.30, F:R.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, N.C. et al., A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site. Nat Commun (2018)

Release Date

2018-02-28

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemagglutinin

Hemagglutinin

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