SMTL ID : 5t6s.1 (1 other biounit)

Crystal structure of the A/Shanghai/2/2013 (H7N9) influenza virus hemagglutinin in complex with the antiviral drug arbidol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

hetero-3-3-mer

Ligands

2 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: 4 residues within 4Å: Chain C: N.28, T.30, T.309 Chain D: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 4 residues within 4Å: Chain E: N.28, T.30, T.309 Chain F: L.52 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 5 residues within 4Å: Chain F: D.147, A.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.147

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

NAG.4: 4 residues within 4Å: Chain A: N.28, T.30, T.309 Chain B: L.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.28, A:N.28 NAG.5: 1 residues within 4Å: Chain A: N.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.231 NAG.8: 5 residues within 4Å: Chain B: E.72, K.75, G.78, N.79, N.82 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.75 Hydrogen bonds: B:E.72 Water bridges: B:N.82, B:N.82 NAG.9: 3 residues within 4Å: Chain B: A.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.154 NAG.10: 1 residues within 4Å: Chain C: N.231 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.231 NAG.11: 5 residues within 4Å: Chain D: E.72, K.75, G.78, N.79, N.82 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:K.75 Hydrogen bonds: D:E.72, D:N.82 Water bridges: D:G.78, D:N.82, D:R.85, D:R.85 NAG.12: 4 residues within 4Å: Chain D: D.147, A.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.154 NAG.13: 2 residues within 4Å: Chain E: K.160, N.231 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.160 NAG.15: 5 residues within 4Å: Chain F: E.72, K.75, G.78, N.79, N.82 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:K.75 Hydrogen bonds: F:E.72, F:N.82 Water bridges: F:K.75

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

75U.6: 17 residues within 4Å: Chain A: P.284, F.285, R.298 Chain B: R.54, L.55, E.57, T.59, W.92, L.99 Chain E: L.19, Q.302 Chain F: E.90, S.93, Y.94, E.97, L.98, A.101 11 PLIP interactions: 6 interactions with chain F, 2 interactions with chain A, 2 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: F:Y.94, F:Y.94, F:E.97, F:A.101, A:P.284, A:F.285, B:R.54, B:L.99, E:L.19 Hydrogen bonds: F:E.90 Salt bridges: F:E.90 75U.7: 16 residues within 4Å: Chain A: Q.302 Chain B: E.90, S.93, Y.94, E.97, L.98, A.101 Chain C: P.284, F.285, R.298 Chain D: R.54, L.55, E.57, T.59, W.92, L.99 12 PLIP interactions: 4 interactions with chain D, 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: D:R.54, D:L.55, D:T.59, D:L.99, B:Y.94, B:Y.94, B:E.97, B:A.101, C:P.284, C:F.285 Hydrogen bonds: B:E.90 Salt bridges: B:E.90 75U.14: 16 residues within 4Å: Chain C: L.19, Q.302 Chain D: E.90, S.93, Y.94, E.97, A.101 Chain E: P.284, F.285 Chain F: R.54, L.55, E.57, T.59, W.92, L.99, E.103 10 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E, 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: F:R.54, F:L.99, E:P.284, E:F.285, C:L.19, D:Y.94, D:A.101 Hydrogen bonds: F:T.59, D:E.90 Salt bridges: D:E.90

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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