SMTL ID : 5t6s.2 (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 Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

hetero-3-3-mer

Ligands

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.1: 4 residues within 4Å: Chain A: N.28, T.30, T.309 Chain B: L.52 No protein-ligand interaction detected (PLIP)

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: 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.3: 4 residues within 4Å: Chain E: N.28, T.30, T.309 Chain F: L.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain F: D.147, A.150, N.154, T.156 No protein-ligand interaction detected (PLIP)

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

75U.5: 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:E.97, B:L.98, B:A.101, C:P.284, C:F.285 Hydrogen bonds: B:E.90 Salt bridges: B:E.90 75U.8: 15 residues within 4Å: Chain C: Q.302 Chain D: E.90, S.93, Y.94, E.97, L.98, A.101 Chain E: P.284, F.285 Chain F: R.54, L.55, E.57, T.59, W.92, L.99 12 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: D:Y.94, D:E.97, D:L.98, D:A.101, E:P.284, E:F.285, F:R.54, F:L.55, F:L.99 Hydrogen bonds: D:E.90 Salt bridges: D:E.90 Water bridges: F:T.59 75U.13: 15 residues within 4Å: Chain A: P.284, F.285 Chain B: R.54, L.55, E.57, T.59, W.92, L.99 Chain E: L.19, Q.302 Chain F: E.90, Y.94, E.97, L.98, A.101 11 PLIP interactions: 3 interactions with chain B, 5 interactions with chain F, 1 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: B:L.55, B:T.59, B:L.99, F:Y.94, F:E.97, F:A.101, E:L.19, A:P.284, A:F.285 Hydrogen bonds: F:E.90 Salt bridges: F:E.90

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

NAG.6: 5 residues within 4Å: Chain B: E.72, K.75, G.78, N.79, N.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.72, B:N.82 NAG.7: 1 residues within 4Å: Chain C: N.231 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.231 NAG.9: 5 residues within 4Å: Chain D: E.72, K.75, G.78, N.79, N.82 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:K.75 Hydrogen bonds: D:E.72, D:N.82 NAG.10: 2 residues within 4Å: Chain D: N.154, T.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.154 NAG.12: 2 residues within 4Å: Chain E: K.160, N.231 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.231 NAG.14: 5 residues within 4Å: Chain F: E.72, K.75, G.78, N.79, N.82 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:K.75 Hydrogen bonds: F:E.72

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 2 residues within 4Å: Chain D: E.128 Chain F: E.128 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.128

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
G

C
I

E
K

B
H

D
J

F
L

Hemagglutinin HA1

Hemagglutinin HA2

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