SMTL ID : 4fnk.1

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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(Post Translational Modification)

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

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, K.293 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: 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(Post Translational Modification)

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

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(Non-functional Binders)

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: 4 residues within 4Å: Chain A: P.15, N.16, E.29, P.318 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.318 Hydrogen bonds: A:E.29 Water bridges: A:N.16, A:N.16 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:N.32, A:T.312 NAG.12: 4 residues within 4Å: Chain A: N.75, E.113, F.114, I.115 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.75, A:E.113, A:E.113, A:F.114 Water bridges: A:N.75, A:N.75, A:F.114 NAG.14: 5 residues within 4Å: Chain B: A.147, E.150, S.151, N.154, T.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.147 Water bridges: B:E.150, B:N.154 NAG.19: 3 residues within 4Å: Chain E: N.32, T.312 Chain F: L.52 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.32, E:T.312 NAG.20: 5 residues within 4Å: Chain E: Q.74, N.75, E.113, F.114, I.115 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.75, E:E.113 NAG.23: 5 residues within 4Å: Chain F: A.147, E.150, S.151, N.154, T.156 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.151, F:N.154 Water bridges: F:T.156

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

SO4.13: 5 residues within 4Å: Chain A: R.201, R.202 Chain C: S.89, V.217, R.218 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:S.89 Water bridges: C:S.89, C:S.89, C:R.218, A:R.201 Salt bridges: C:R.218, A:R.201, A:R.202 SO4.15: 5 residues within 4Å: Chain B: R.127, H.159, D.160 Chain D: M.133, K.139 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:Y.141, B:D.160 Water bridges: D:K.139, B:R.127 Salt bridges: D:K.139, B:R.127, B:H.159 SO4.17: 4 residues within 4Å: Chain D: W.14, E.15, G.16, R.25 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.15, D:G.16 Salt bridges: D:R.25 SO4.18: 4 residues within 4Å: Chain D: R.127, H.159, D.160 Chain F: K.139 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain F Water bridges: D:R.127, D:R.127, F:K.139, F:K.139 Salt bridges: D:R.127, D:H.159, F:K.139 SO4.21: 4 residues within 4Å: Chain A: S.89, V.217, R.218 Chain E: R.202 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain A Salt bridges: E:R.202, A:R.218 Hydrogen bonds: A:S.89 Water bridges: A:S.89, A:R.218 SO4.24: 6 residues within 4Å: Chain B: M.133, K.139, Y.141 Chain F: R.127, H.159, D.160 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain B Water bridges: F:R.127, F:R.127, B:K.139, B:Y.141 Salt bridges: F:R.127, F:H.159, B:K.139 Hydrogen bonds: B:Y.141

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 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 Water bridges: C:R.84, C:D.265 GOL.22: 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 Water bridges: E:D.265, E:I.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ekiert, D.C. et al., Cross-neutralization of influenza A viruses mediated by a single antibody loop. Nature (2012)

Release Date

2012-09-19

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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