SMTL ID : 4we4.1

The crystal structure of hemagglutinin from 1968 H3N2 influenza virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-NAG-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-NAG-MAN.15: 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-NAG-MAN.29: 4 residues within 4Å: Chain E: N.30, T.32, T.310 Chain F: L.52 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.2: 5 residues within 4Å: Chain A: N.157, T.159 Chain C: S.211, P.213, W.214 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:T.159 Hydrogen bonds: C:W.214 NAG-NAG-BMA-MAN-MAN.16: 5 residues within 4Å: Chain C: N.157, T.159 Chain E: S.211, P.213, W.214 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:T.159 Hydrogen bonds: E:W.214 NAG-NAG-BMA-MAN-MAN.30: 5 residues within 4Å: Chain A: S.211, P.213, W.214 Chain E: N.157, T.159 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:T.159 Hydrogen bonds: A:W.214

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.3: 5 residues within 4Å: Chain A: S.37, N.277, V.289, N.290 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 5 residues within 4Å: Chain C: S.37, N.277, V.289, N.290 Chain D: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 5 residues within 4Å: Chain E: S.37, N.277, V.289, N.290 Chain F: E.69 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 3 residues within 4Å: Chain B: A.147, E.150, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain D: A.147, E.150, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain F: A.147, E.150, N.154 No protein-ligand interaction detected (PLIP)

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

NAG.5: 3 residues within 4Å: Chain A: N.14, T.16, T.29 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.16 Hydrogen bonds: A:N.14 NAG.6: 3 residues within 4Å: Chain A: Q.72, N.73, F.112 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.72 Hydrogen bonds: A:Q.72, A:N.73 Water bridges: A:T.114 NAG.19: 3 residues within 4Å: Chain C: N.14, T.16, T.29 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.16 Hydrogen bonds: C:N.14 NAG.20: 3 residues within 4Å: Chain C: Q.72, N.73, F.112 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Q.72 Hydrogen bonds: C:Q.72, C:N.73 Water bridges: C:T.114 NAG.33: 3 residues within 4Å: Chain E: N.14, T.16, T.29 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.16 Hydrogen bonds: E:N.14 NAG.34: 3 residues within 4Å: Chain E: Q.72, N.73, F.112 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Q.72 Hydrogen bonds: E:Q.72, E:N.73 Water bridges: E:T.114

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

PEG.7: 7 residues within 4Å: Chain A: M.260, R.261, I.292 Chain B: E.67, K.68, E.69 Ligands: PEG.8 Ligand excluded by PLIP PEG.8: 10 residues within 4Å: Chain A: I.259, M.260, K.291, I.292, T.293 Chain B: Q.65, I.66, E.67, K.68 Ligands: PEG.7 Ligand excluded by PLIP PEG.9: 7 residues within 4Å: Chain B: E.69, F.70, E.72, V.73, Q.78, K.82 Ligands: PEG.12 Ligand excluded by PLIP PEG.10: 9 residues within 4Å: Chain A: K.291 Chain B: I.66, E.67, K.68, F.70, E.81, K.82, E.85, D.86 Ligand excluded by PLIP PEG.11: 7 residues within 4Å: Chain B: D.79, K.82, Y.83, D.86 Chain F: H.64, Q.65 Ligands: PEG.12 Ligand excluded by PLIP PEG.12: 8 residues within 4Å: Chain B: V.73, E.74, G.75, Q.78, D.79, K.82 Ligands: PEG.9, PEG.11 Ligand excluded by PLIP PEG.13: 3 residues within 4Å: Chain A: K.299 Chain B: R.54, V.55 Ligand excluded by PLIP PEG.21: 7 residues within 4Å: Chain C: M.260, R.261, I.292 Chain D: E.67, K.68, E.69 Ligands: PEG.22 Ligand excluded by PLIP PEG.22: 10 residues within 4Å: Chain C: I.259, M.260, K.291, I.292, T.293 Chain D: Q.65, I.66, E.67, K.68 Ligands: PEG.21 Ligand excluded by PLIP PEG.23: 7 residues within 4Å: Chain D: E.69, F.70, E.72, V.73, Q.78, K.82 Ligands: PEG.26 Ligand excluded by PLIP PEG.24: 9 residues within 4Å: Chain C: K.291 Chain D: I.66, E.67, K.68, F.70, E.81, K.82, E.85, D.86 Ligand excluded by PLIP PEG.25: 7 residues within 4Å: Chain B: H.64, Q.65 Chain D: D.79, K.82, Y.83, D.86 Ligands: PEG.26 Ligand excluded by PLIP PEG.26: 8 residues within 4Å: Chain D: V.73, E.74, G.75, Q.78, D.79, K.82 Ligands: PEG.23, PEG.25 Ligand excluded by PLIP PEG.27: 3 residues within 4Å: Chain C: K.299 Chain D: R.54, V.55 Ligand excluded by PLIP PEG.35: 7 residues within 4Å: Chain E: M.260, R.261, I.292 Chain F: E.67, K.68, E.69 Ligands: PEG.36 Ligand excluded by PLIP PEG.36: 10 residues within 4Å: Chain E: I.259, M.260, K.291, I.292, T.293 Chain F: Q.65, I.66, E.67, K.68 Ligands: PEG.35 Ligand excluded by PLIP PEG.37: 7 residues within 4Å: Chain F: E.69, F.70, E.72, V.73, Q.78, K.82 Ligands: PEG.40 Ligand excluded by PLIP PEG.38: 9 residues within 4Å: Chain E: K.291 Chain F: I.66, E.67, K.68, F.70, E.81, K.82, E.85, D.86 Ligand excluded by PLIP PEG.39: 7 residues within 4Å: Chain D: H.64, Q.65 Chain F: D.79, K.82, Y.83, D.86 Ligands: PEG.40 Ligand excluded by PLIP PEG.40: 8 residues within 4Å: Chain F: V.73, E.74, G.75, Q.78, D.79, K.82 Ligands: PEG.37, PEG.39 Ligand excluded by PLIP PEG.41: 3 residues within 4Å: Chain E: K.299 Chain F: R.54, V.55 Ligand excluded by PLIP

3 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.14: 16 residues within 4Å: Chain A: Y.97, A.98, R.101, S.102, R.261 Chain B: H.64, Q.65, I.66, E.67, F.70, S.71, E.72, E.74, E.81 Chain D: R.76, D.79 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:R.101, A:S.102, A:R.261, B:E.67, B:E.67, B:S.71, B:S.71, B:E.72, B:E.72, B:E.74 Water bridges: B:S.71, B:E.74 PE5.28: 16 residues within 4Å: Chain C: Y.97, A.98, R.101, S.102, R.261 Chain D: H.64, Q.65, I.66, E.67, F.70, S.71, E.72, E.74, E.81 Chain F: R.76, D.79 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:R.101, C:S.102, C:R.261, D:E.67, D:S.71, D:S.71, D:E.72, D:E.74 Water bridges: D:S.71, D:E.74 PE5.42: 16 residues within 4Å: Chain B: R.76, D.79 Chain E: Y.97, A.98, R.101, S.102, R.261 Chain F: H.64, Q.65, I.66, E.67, F.70, S.71, E.72, E.74, E.81 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:E.67, F:S.71, F:S.71, F:E.72, F:E.72, F:E.74, E:R.101, E:S.102, E:R.261 Water bridges: F:S.71, F:E.74

Links

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Citation

Yang, H. et al., Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins. Virology (2015)

Release Date

2015-02-11

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