SMTL ID : 5t6n.1

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in complex with the antiviral drug arbidol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

hetero-3-3-mer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 6 residues within 4Å: Chain A: N.159, T.161 Chain C: S.213, R.214, P.215, W.216 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: 5 residues within 4Å: Chain A: S.39, N.279, V.291, N.292 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.32, T.34, T.312 Chain D: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain C: N.75, E.113, F.114, I.115, F.168, Y.251 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.115, C:F.168 NAG-NAG.6: 5 residues within 4Å: Chain C: S.39, N.279, V.291, N.292 Chain D: E.69 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.293 NAG-NAG.7: 4 residues within 4Å: Chain D: A.147, E.150, N.154, T.156 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain E: S.39, N.279, V.291, N.292, K.293 Chain F: E.69 No protein-ligand interaction detected (PLIP)

1 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.5: 7 residues within 4Å: Chain C: N.159, T.161, V.236 Chain E: S.213, R.214, P.215, W.216 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:V.236 Hydrogen bonds: E:W.216

1 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.8: 5 residues within 4Å: Chain A: S.213, P.215, W.216 Chain E: N.159, T.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.216

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

NAG.10: 3 residues within 4Å: Chain A: P.15, N.16, E.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.29 NAG.11: 3 residues within 4Å: Chain A: N.32, T.312 Chain B: L.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.312 Water bridges: A:N.32 NAG.12: 3 residues within 4Å: Chain A: N.75, E.113, F.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.113, A:E.113 NAG.14: 4 residues within 4Å: Chain B: A.147, E.150, N.154, T.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.150, B:N.154 NAG.22: 2 residues within 4Å: Chain E: N.32, T.312 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.312 NAG.23: 5 residues within 4Å: Chain E: Q.74, N.75, E.113, F.114, I.115 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.75 Water bridges: E:F.114, E:R.144 NAG.25: 5 residues within 4Å: Chain F: A.147, E.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.154

3 x 75U: ethyl 6-bromo-4-[(dimethylamino)methyl]-5-hydroxy-1-methyl-2-[(phenylsulfanyl)methyl]-1H-indole-3-carboxylate(Non-covalent)

75U.13: 17 residues within 4Å: Chain A: I.23, K.304, Q.305 Chain B: D.90, S.93, Y.94, E.97, L.98, A.101 Chain E: F.288, K.301 Chain F: R.54, V.55, E.57, K.58, T.59, W.92 8 PLIP interactions: 4 interactions with chain B, 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: B:Y.94, B:E.97, B:A.101, E:F.288, A:I.23 Salt bridges: B:D.90, E:K.301 Hydrogen bonds: E:K.301 75U.19: 13 residues within 4Å: Chain A: F.288, K.301 Chain B: R.54, V.55, E.57 Chain C: K.304, Q.305 Chain D: D.90, S.93, Y.94, E.97, L.98, A.101 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.94, D:E.97, D:A.101, A:F.288 Salt bridges: D:D.90, A:K.301 Hydrogen bonds: A:K.301 75U.20: 17 residues within 4Å: Chain C: P.287, F.288, K.301 Chain D: R.54, V.55, E.57, K.58, T.59, W.92 Chain E: I.23, K.304, Q.305 Chain F: D.90, S.93, Y.94, E.97, A.101 8 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 3 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: D:R.54, D:T.59, C:P.287, C:F.288, F:Y.94, F:A.101, E:I.23 Salt bridges: F:D.90

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

SO4.15: 4 residues within 4Å: Chain B: K.139 Chain F: R.127, H.159, D.160 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:D.160 Salt bridges: F:R.127, F:H.159, B:K.139 SO4.16: 4 residues within 4Å: Chain B: R.127, H.159, D.160 Chain D: K.139 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:D.160 Salt bridges: B:R.127, B:H.159, D:K.139 Water bridges: D:K.139 SO4.17: 4 residues within 4Å: Chain A: R.202 Chain C: S.89, V.217, R.218 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.89 Water bridges: C:S.89, C:S.89, C:Y.94 Salt bridges: C:R.218, A:R.202 SO4.21: 4 residues within 4Å: Chain D: R.127, H.159, D.160 Chain F: K.139 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Salt bridges: F:K.139, D:R.127, D:H.159

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 4 residues within 4Å: Chain C: R.84, K.86, D.265, P.267 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.86, C:K.86, C:D.265 Water bridges: C:D.54 GOL.24: 4 residues within 4Å: Chain E: R.84, K.86, D.265, P.267 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.86, E:K.86, E:D.265 Water bridges: E:I.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadam, R.U. et al., Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-01-04

Peptides

Hemagglutinin HA1: ACE
Hemagglutinin HA2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin HA1

Hemagglutinin HA2

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