SMTL ID : 8tj9.1

CRYSTAL STRUCTURE OF THE A/Michigan/15/2014(H3N2) INFLUENZA VIRUS HEMAGGLUTININ WITH HUMAN RECEPTOR ANALOG 6'-SLNLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-3-3-mer

Ligands

9 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.1: 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-BMA.2 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.216, C:K.216 Hydrophobic interactions: A:I.236 NAG-NAG-BMA.2: 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-BMA.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 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-BMA.21 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:K.216, E:K.216 Hydrophobic interactions: C:I.236 NAG-NAG-BMA.21: 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-BMA.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 4 residues within 4Å: Chain C: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 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-BMA.40 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:K.216, A:K.216 Hydrophobic interactions: E:I.236 NAG-NAG-BMA.40: 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-BMA.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 4 residues within 4Å: Chain E: N.39, N.279, V.291, N.292 No protein-ligand interaction detected (PLIP)

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

NAG-GAL-NAG-GAL-SIA.4: 14 residues within 4Å: Chain A: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, Y.153, H.177, 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 Hydrogen bonds: A:D.219, A:T.129, A:S.131, A:S.222, A:S.222 NAG-GAL-NAG-GAL-SIA.23: 14 residues within 4Å: Chain C: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, Y.153, H.177, 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 Hydrogen bonds: C:D.219, C:T.129, C:S.131, C:S.222, C:S.222 NAG-GAL-NAG-GAL-SIA.42: 14 residues within 4Å: Chain E: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, Y.153, H.177, 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 Hydrogen bonds: E:D.219, E:T.129, E:S.131, E:S.222, E:S.222

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

NAG.5: 3 residues within 4Å: Chain A: N.32, T.312 Chain B: L.52 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.32, A:N.32 NAG.6: 2 residues within 4Å: Chain A: 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: N.127, R.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.127, A:R.249 NAG.24: 3 residues within 4Å: Chain C: N.32, T.312 Chain D: L.52 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.32, C:N.32 NAG.25: 2 residues within 4Å: Chain C: 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.26: 2 residues within 4Å: Chain C: N.127, R.249 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.127, C:R.249 NAG.43: 3 residues within 4Å: Chain E: N.32, T.312 Chain F: L.52 2 PLIP interactions: 2 interactions with chain E Water bridges: E:N.32, E:N.32 NAG.44: 2 residues within 4Å: Chain E: 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.45: 2 residues within 4Å: Chain E: N.127, R.249 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.127, E:R.249

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

PEG.8: 4 residues within 4Å: Chain A: Q.167, D.169, K.232, P.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.169 PEG.9: 3 residues within 4Å: Chain A: E.35, N.39, K.286 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.39, A:N.39, A:K.286, A:K.286 Water bridges: A:E.35, A:N.39 PEG.15: 7 residues within 4Å: Chain B: Q.105, H.106, D.109 Chain D: L.102 Chain F: H.106 Ligands: PEG.34, PEG.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.109 PEG.27: 4 residues within 4Å: Chain C: Q.167, D.169, K.232, P.233 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.169 PEG.28: 3 residues within 4Å: Chain C: E.35, N.39, K.286 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.39, C:N.39, C:K.286, C:K.286 Water bridges: C:E.35, C:N.39 PEG.34: 7 residues within 4Å: Chain B: H.106 Chain D: Q.105, H.106, D.109 Chain F: L.102 Ligands: PEG.15, PEG.53 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.109 PEG.46: 4 residues within 4Å: Chain E: Q.167, D.169, K.232, P.233 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.169 PEG.47: 3 residues within 4Å: Chain E: E.35, N.39, K.286 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.39, E:N.39, E:K.286, E:K.286 Water bridges: E:E.35, E:N.39 PEG.53: 7 residues within 4Å: Chain B: L.102 Chain D: H.106 Chain F: Q.105, H.106, D.109 Ligands: PEG.15, PEG.34 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.109

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

SO4.10: 1 residues within 4Å: Chain A: Y.99 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:S.71, A:Y.99 SO4.11: 6 residues within 4Å: Chain A: E.117, S.118, F.119, N.120, W.121, Q.126 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.118, A:F.119, A:N.120, A:W.121, A:Q.126, A:Q.126 SO4.18: 4 residues within 4Å: Chain B: W.14, E.15, G.16, R.25 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.15, B:G.16 Water bridges: B:N.12, A:E.319 Salt bridges: B:R.25 SO4.19: 6 residues within 4Å: Chain B: M.133, K.139, Y.141 Chain F: R.127, H.159, N.160 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:N.160, B:Y.141 Salt bridges: F:R.127, F:H.159, B:K.139 SO4.29: 1 residues within 4Å: Chain C: Y.99 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:S.71, C:Y.99 SO4.30: 6 residues within 4Å: Chain C: E.117, S.118, F.119, N.120, W.121, Q.126 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.118, C:F.119, C:N.120, C:W.121, C:Q.126, C:Q.126 SO4.37: 4 residues within 4Å: Chain D: W.14, E.15, G.16, R.25 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.15, D:G.16 Water bridges: D:N.12, C:E.319 Salt bridges: D:R.25 SO4.38: 6 residues within 4Å: Chain B: R.127, H.159, N.160 Chain D: M.133, K.139, Y.141 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:Y.141, B:N.160 Salt bridges: D:K.139, B:R.127, B:H.159 SO4.48: 1 residues within 4Å: Chain E: Y.99 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Water bridges: F:S.71, E:Y.99 SO4.49: 6 residues within 4Å: Chain E: E.117, S.118, F.119, N.120, W.121, Q.126 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.118, E:F.119, E:N.120, E:W.121, E:Q.126, E:Q.126 SO4.56: 4 residues within 4Å: Chain F: W.14, E.15, G.16, R.25 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain F Water bridges: E:E.319, F:N.12 Hydrogen bonds: F:E.15, F:G.16 Salt bridges: F:R.25 SO4.57: 6 residues within 4Å: Chain D: R.127, H.159, N.160 Chain F: M.133, K.139, Y.141 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:Y.141, D:N.160 Salt bridges: F:K.139, D:R.127, D:H.159

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 3 residues within 4Å: Chain B: R.25, R.32, G.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.32 EDO.14: 4 residues within 4Å: Chain A: R.263 Chain B: E.69, F.70, S.71 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.71, A:R.263 Hydrogen bonds: A:R.263 EDO.16: 3 residues within 4Å: Chain B: M.133, G.134, N.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.133 EDO.31: 3 residues within 4Å: Chain D: R.25, R.32, G.33 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.32 EDO.33: 4 residues within 4Å: Chain C: R.263 Chain D: E.69, F.70, S.71 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:S.71, C:R.263 Hydrogen bonds: C:R.263 EDO.35: 3 residues within 4Å: Chain D: M.133, G.134, N.135 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.133 EDO.50: 3 residues within 4Å: Chain F: R.25, R.32, G.33 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.32 EDO.52: 4 residues within 4Å: Chain E: R.263 Chain F: E.69, F.70, S.71 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Water bridges: F:S.71, E:R.263 Hydrogen bonds: E:R.263 EDO.54: 3 residues within 4Å: Chain F: M.133, G.134, N.135 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:M.133

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.13: 8 residues within 4Å: Chain A: R.301 Chain B: R.54, L.55, W.92 Chain D: Y.94, E.97, L.98, A.101 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.54, A:R.301 Water bridges: B:N.60, A:R.301 PG4.32: 8 residues within 4Å: Chain C: R.301 Chain D: R.54, L.55, W.92 Chain F: Y.94, E.97, L.98, A.101 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.54, C:R.301 Water bridges: D:N.60, C:R.301 PG4.51: 8 residues within 4Å: Chain B: Y.94, E.97, L.98, A.101 Chain E: R.301 Chain F: R.54, L.55, W.92 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:R.301, F:R.54 Water bridges: E:R.301, F:N.60

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.17: 7 residues within 4Å: Chain A: H.12 Chain B: M.17, V.18, D.19, G.20, W.21, T.41 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.17, A:H.12 PGE.36: 7 residues within 4Å: Chain C: H.12 Chain D: M.17, V.18, D.19, G.20, W.21, T.41 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.12, D:M.17 PGE.55: 7 residues within 4Å: Chain E: H.12 Chain F: M.17, V.18, D.19, G.20, W.21, T.41 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:H.12, F:M.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.J. et al., Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site. Cell Host Microbe (2024)

Release Date

2024-02-14

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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