SMTL ID : 8tja.1

CRYSTAL STRUCTURE OF THE A/Ecuador/1374/2016(H3N2) INFLUENZA VIRUS HEMAGGLUTININ WITH HUMAN RECEPTOR ANALOG 6'-SLNLN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-3-3-mer

Ligands

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.1: 8 residues within 4Å: Chain A: N.159, T.161 Chain E: T.181, S.213, P.215, R.216 Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.216 Water bridges: E:R.216 NAG-NAG-BMA-MAN-MAN.25: 8 residues within 4Å: Chain A: T.181, S.213, P.215, R.216 Chain C: N.159, T.161 Ligands: NAG-NAG-BMA.26, NAG-NAG-BMA.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.216 Water bridges: A:R.216 NAG-NAG-BMA-MAN-MAN.49: 8 residues within 4Å: Chain C: T.181, S.213, P.215, R.216 Chain E: N.159, T.161 Ligands: NAG-NAG-BMA.50, NAG-NAG-BMA.50 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.216 Water bridges: C:R.216

3 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.2: 10 residues within 4Å: Chain A: A.157, L.158, N.159, R.195, N.240, S.241, T.242 Chain E: K.183, I.211 Ligands: NAG-NAG-BMA-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 10 residues within 4Å: Chain A: K.183, I.211 Chain C: A.157, L.158, N.159, R.195, N.240, S.241, T.242 Ligands: NAG-NAG-BMA-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.50: 10 residues within 4Å: Chain C: K.183, I.211 Chain E: A.157, L.158, N.159, R.195, N.240, S.241, T.242 Ligands: NAG-NAG-BMA-MAN-MAN.49 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.3: 14 residues within 4Å: Chain A: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, H.177, S.187, L.188, R.216, D.219, I.220, S.222 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.188, A:W.147, A:T.149, A:L.188 Water bridges: A:D.184, A:T.129, A:T.129, A:S.131 Hydrogen bonds: A:R.216, A:D.219, A:Y.92, A:T.129, A:S.131, A:S.222, A:S.222 NAG-GAL-NAG-GAL-SIA.27: 14 residues within 4Å: Chain C: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, H.177, S.187, L.188, R.216, D.219, I.220, S.222 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.188, C:W.147, C:T.149, C:L.188 Water bridges: C:D.184, C:T.129, C:T.129, C:S.131 Hydrogen bonds: C:R.216, C:D.219, C:Y.92, C:T.129, C:S.131, C:S.222, C:S.222 NAG-GAL-NAG-GAL-SIA.51: 14 residues within 4Å: Chain E: Y.92, G.128, T.129, S.130, S.131, W.147, T.149, H.177, S.187, L.188, R.216, D.219, I.220, S.222 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:L.188, E:W.147, E:T.149, E:L.188 Water bridges: E:D.184, E:T.129, E:T.129, E:S.131 Hydrogen bonds: E:R.216, E:D.219, E:Y.92, E:T.129, E:S.131, E:S.222, E:S.222

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

NAG.4: 3 residues within 4Å: Chain A: E.56, N.57, Y.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.57 Water bridges: A:N.57 NAG.5: 4 residues within 4Å: Chain A: N.39, N.279, V.291, N.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.279, A:V.291, A:N.292 Water bridges: A:V.291 NAG.6: 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.7: 6 residues within 4Å: Chain A: N.32, T.34, T.312 Chain B: L.52 Ligands: PG4.8, PEG.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32, A:T.312 NAG.28: 3 residues within 4Å: Chain C: E.56, N.57, Y.88 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.57 Water bridges: C:N.57 NAG.29: 4 residues within 4Å: Chain C: N.39, N.279, V.291, N.292 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.279, C:V.291, C:N.292 Water bridges: C:V.291 NAG.30: 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.31: 6 residues within 4Å: Chain C: N.32, T.34, T.312 Chain D: L.52 Ligands: PG4.32, PEG.45 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.32, C:T.312 NAG.52: 3 residues within 4Å: Chain E: E.56, N.57, Y.88 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.57 Water bridges: E:N.57 NAG.53: 4 residues within 4Å: Chain E: N.39, N.279, V.291, N.292 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.279, E:V.291, E:N.292 Water bridges: E:V.291 NAG.54: 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 NAG.55: 6 residues within 4Å: Chain E: N.32, T.34, T.312 Chain F: L.52 Ligands: PG4.56, PEG.69 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.32, E:T.312

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

PG4.8: 11 residues within 4Å: Chain A: H.12, T.31, N.32, T.312 Chain B: V.18, D.19, G.20, W.21, I.45 Ligands: NAG.7, PEG.21 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.31, A:N.32, B:G.20 PG4.13: 8 residues within 4Å: Chain A: F.288, R.301 Chain B: R.54, L.55, W.92, E.103 Chain E: I.23 Chain F: Y.94 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:R.301, E:I.23 Water bridges: A:R.301 PG4.32: 11 residues within 4Å: Chain C: H.12, T.31, N.32, T.312 Chain D: V.18, D.19, G.20, W.21, I.45 Ligands: NAG.31, PEG.45 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.20, C:T.31, C:N.32 PG4.37: 8 residues within 4Å: Chain A: I.23 Chain B: Y.94 Chain C: F.288, R.301 Chain D: R.54, L.55, W.92, E.103 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.301, A:I.23 Water bridges: C:R.301 PG4.56: 11 residues within 4Å: Chain E: H.12, T.31, N.32, T.312 Chain F: V.18, D.19, G.20, W.21, I.45 Ligands: NAG.55, PEG.69 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.31, E:N.32, F:G.20 PG4.61: 8 residues within 4Å: Chain C: I.23 Chain D: Y.94 Chain E: F.288, R.301 Chain F: R.54, L.55, W.92, E.103 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:R.301, C:I.23 Water bridges: E:R.301

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

EDO.9: 5 residues within 4Å: Chain A: K.77, W.78, D.79, G.110, S.259 Ligand excluded by PLIP EDO.10: 1 residues within 4Å: Chain A: S.48 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: P.93, Y.94, I.217, R.223 Chain C: K.201 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: C.299, R.301 Chain B: T.59, N.60, K.62 Ligand excluded by PLIP EDO.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Chain B: S.29 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: H.26, N.146, R.153 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: G.155, D.158 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: D.79, K.82, Y.83 Chain D: H.64, Q.65 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain C: K.77, W.78, D.79, G.110, S.259 Ligand excluded by PLIP EDO.34: 1 residues within 4Å: Chain C: S.48 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain C: P.93, Y.94, I.217, R.223 Chain E: K.201 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain C: C.299, R.301 Chain D: T.59, N.60, K.62 Ligand excluded by PLIP EDO.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.40: 1 residues within 4Å: Chain D: S.29 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain D: H.26, N.146, R.153 Ligand excluded by PLIP EDO.42: 2 residues within 4Å: Chain D: G.155, D.158 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain D: D.79, K.82, Y.83 Chain F: H.64, Q.65 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain E: K.77, W.78, D.79, G.110, S.259 Ligand excluded by PLIP EDO.58: 1 residues within 4Å: Chain E: S.48 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain A: K.201 Chain E: P.93, Y.94, I.217, R.223 Ligand excluded by PLIP EDO.62: 5 residues within 4Å: Chain E: C.299, R.301 Chain F: T.59, N.60, K.62 Ligand excluded by PLIP EDO.63: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.64: 1 residues within 4Å: Chain F: S.29 Ligand excluded by PLIP EDO.65: 3 residues within 4Å: Chain F: H.26, N.146, R.153 Ligand excluded by PLIP EDO.66: 2 residues within 4Å: Chain F: G.155, D.158 Ligand excluded by PLIP EDO.67: 5 residues within 4Å: Chain B: H.64, Q.65 Chain F: D.79, K.82, Y.83 Ligand excluded by PLIP

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

PEG.12: 2 residues within 4Å: Chain A: R.315 Chain B: A.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.315, A:R.315 PEG.20: 4 residues within 4Å: Chain A: R.263 Chain B: E.69, F.70, S.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.71 PEG.21: 7 residues within 4Å: Chain A: T.312 Chain B: I.45, I.48, N.49, L.52 Ligands: NAG.7, PG4.8 No protein-ligand interaction detected (PLIP) PEG.22: 6 residues within 4Å: Chain B: G.8, F.9, E.11, M.133, G.134, N.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.11 PEG.36: 2 residues within 4Å: Chain C: R.315 Chain D: A.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.315, C:R.315 PEG.44: 4 residues within 4Å: Chain C: R.263 Chain D: E.69, F.70, S.71 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.71 PEG.45: 7 residues within 4Å: Chain C: T.312 Chain D: I.45, I.48, N.49, L.52 Ligands: NAG.31, PG4.32 No protein-ligand interaction detected (PLIP) PEG.46: 6 residues within 4Å: Chain D: G.8, F.9, E.11, M.133, G.134, N.135 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.11 PEG.60: 2 residues within 4Å: Chain E: R.315 Chain F: A.7 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.315, E:R.315 PEG.68: 4 residues within 4Å: Chain E: R.263 Chain F: E.69, F.70, S.71 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.71 PEG.69: 7 residues within 4Å: Chain E: T.312 Chain F: I.45, I.48, N.49, L.52 Ligands: NAG.55, PG4.56 No protein-ligand interaction detected (PLIP) PEG.70: 6 residues within 4Å: Chain F: G.8, F.9, E.11, M.133, G.134, N.135 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.11

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

SO4.23: 5 residues within 4Å: Chain B: M.133, K.139 Chain D: R.127, H.159, N.160 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Y.141, D:N.160 Salt bridges: B:K.139, D:R.127, D:H.159 SO4.24: 5 residues within 4Å: Chain B: G.13, W.14, E.15, G.16, R.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.15, B:G.16 Salt bridges: B:R.25 SO4.47: 5 residues within 4Å: Chain D: M.133, K.139 Chain F: R.127, H.159, N.160 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:Y.141, F:N.160 Salt bridges: D:K.139, F:R.127, F:H.159 SO4.48: 5 residues within 4Å: Chain D: G.13, W.14, E.15, G.16, R.25 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.15, D:G.16 Salt bridges: D:R.25 SO4.71: 5 residues within 4Å: Chain B: R.127, H.159, N.160 Chain F: M.133, K.139 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:N.160, F:Y.141 Salt bridges: B:R.127, B:H.159, F:K.139 SO4.72: 5 residues within 4Å: Chain F: G.13, W.14, E.15, G.16, R.25 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.15, F:G.16 Salt bridges: F:R.25

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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