SMTL ID : 6cex.1

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in complex with small molecule N-Cyclohexyltaurine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 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: 6 residues within 4Å: Chain A: N.159, T.161 Chain C: S.213, R.214, P.215, W.216 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.216 NAG-NAG-BMA.5: 6 residues within 4Å: Chain C: N.159, T.161, V.236 Chain E: S.213, 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

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: 6 residues within 4Å: Chain A: S.39, N.279, V.291, N.292, K.293 Chain B: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain C: T.31, N.32 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.75, E.113, F.114, I.115 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: S.39, N.279, V.291 Chain D: E.69 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain D: A.147, E.150, S.151, N.154, T.156 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain E: S.39, N.279, V.291, N.292 Chain F: E.69 No protein-ligand interaction detected (PLIP)

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

6 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.10: 7 residues within 4Å: Chain A: G.128, G.129, S.130, N.131, W.147, T.149, L.220 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.147, A:W.147, A:T.149 Hydrogen bonds: A:N.131 NHE.16: 8 residues within 4Å: Chain A: K.301 Chain B: R.54, L.99, E.103 Chain D: Y.94, E.97, L.98, A.101 7 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:E.97, D:L.98, D:A.101, B:L.99 Hydrogen bonds: B:R.54 Water bridges: C:K.304 Salt bridges: A:K.301 NHE.19: 7 residues within 4Å: Chain C: G.128, G.129, S.130, N.131, W.147, T.149, L.220 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.147, C:W.147, C:T.149 Hydrogen bonds: C:N.131 NHE.20: 8 residues within 4Å: Chain C: K.301 Chain D: R.54, L.99 Chain E: I.23 Chain F: Y.94, E.97, L.98, A.101 11 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C, 5 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: D:L.99, F:E.97, F:L.98, F:A.101, E:I.23 Hydrogen bonds: D:R.54 Water bridges: C:K.301, C:K.301, F:Y.94, F:Y.94 Salt bridges: C:K.301 NHE.24: 7 residues within 4Å: Chain E: G.128, G.129, S.130, N.131, W.147, T.149, L.220 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:W.147, E:T.149 Hydrogen bonds: E:N.131, E:N.131 Water bridges: E:Y.92, E:Y.92 NHE.28: 8 residues within 4Å: Chain B: Y.94, E.97, L.98, A.101 Chain E: K.301 Chain F: R.54, K.58, L.99 8 PLIP interactions: 3 interactions with chain B, 2 interactions with chain F, 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: B:E.97, B:L.98, B:A.101, F:L.99 Hydrogen bonds: F:R.54 Water bridges: A:K.304, A:K.304 Salt bridges: E:K.301

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

NAG.11: 3 residues within 4Å: Chain A: P.15, N.16, E.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.16, A:E.29 NAG.12: 2 residues within 4Å: Chain A: N.32, T.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.32, A:T.312 NAG.13: 3 residues within 4Å: Chain A: N.75, E.113, F.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.114 Water bridges: A:N.75 NAG.17: 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.25: 2 residues within 4Å: Chain E: N.32, T.312 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.32, E:T.312 NAG.26: 5 residues within 4Å: Chain E: Q.74, N.75, E.113, F.114, I.115 2 PLIP interactions: 2 interactions with chain E Water bridges: E:Q.74, E:R.144 NAG.27: 4 residues within 4Å: Chain E: P.15, N.16, E.29, P.318 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:P.318 Hydrogen bonds: E:N.16, E:E.29 NAG.29: 5 residues within 4Å: Chain F: A.147, E.150, S.151, N.154, T.156 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.151, F:N.154

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

SO4.14: 4 residues within 4Å: Chain A: C.8 Chain B: R.25, H.26, Q.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.25 SO4.15: 6 residues within 4Å: Chain A: S.89, P.93, Y.94, R.218 Chain E: R.201, R.202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.89, A:Y.94 Water bridges: A:R.218 Salt bridges: A:R.218 SO4.18: 4 residues within 4Å: Chain B: R.127, H.159, D.160 Chain D: K.139 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Salt bridges: D:K.139, B:R.127, B:H.159 Hydrogen bonds: B:D.160 SO4.22: 4 residues within 4Å: Chain D: W.14, E.15, G.16, R.25 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.16 Salt bridges: D:R.25 SO4.23: 4 residues within 4Å: Chain D: R.127, H.159, D.160 Chain F: K.139 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F Salt bridges: D:R.127, D:H.159, F:K.139 Water bridges: F:K.139, F:K.139 SO4.30: 4 residues within 4Å: Chain B: K.139 Chain F: R.127, H.159, D.160 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:D.160 Salt bridges: F:R.127, F:H.159, B:K.139 Water bridges: B:K.139

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 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:I.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadam, R.U. et al., A small-molecule fragment that emulates binding of receptor and broadly neutralizing antibodies to influenza A hemagglutinin. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-04-04

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin

Hemagglutinin

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