SMTL ID : 8pk3.1

CryoEM reconstruction of hemagglutinin HK68 of Influenza A virus bound to an Affimer reagent

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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: 3 residues within 4Å: Chain A: N.75, F.114, T.116 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.116 NAG-NAG.3: 2 residues within 4Å: Chain D: N.75, F.114 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain G: N.75, F.114, T.116 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:T.116

3 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.2: 7 residues within 4Å: Chain A: N.159, T.161, V.236, V.238 Chain G: S.213, W.216 Chain I: Y.37 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:V.236 Hydrogen bonds: G:W.216 NAG-NAG-BMA-MAN-MAN.4: 7 residues within 4Å: Chain A: S.213, W.216 Chain C: Y.37 Chain D: N.159, T.161, V.236, V.238 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:V.236 Hydrogen bonds: A:W.216 NAG-NAG-BMA-MAN-MAN.6: 8 residues within 4Å: Chain D: S.213, P.215, W.216 Chain F: Y.37 Chain G: N.159, T.161, V.236, V.238 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:P.215, G:V.236 Hydrogen bonds: D:W.216

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

NAG.7: 3 residues within 4Å: Chain A: S.39, N.279, N.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.292 NAG.8: 1 residues within 4Å: Chain A: N.32 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain D: S.39, N.279, N.292 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.292 NAG.10: 1 residues within 4Å: Chain D: N.32 No protein-ligand interaction detected (PLIP) NAG.11: 4 residues within 4Å: Chain G: S.39, N.279, V.291, N.292 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:V.291 Hydrogen bonds: G:N.292 NAG.12: 1 residues within 4Å: Chain G: N.32 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Debski-Antoniak, O. et al., Exploiting the Affimer platform against influenza A virus. To Be Published

Release Date

2024-01-03

Peptides

Hemagglutinin HA1 chain: ADG
Hemagglutinin HA2 chain: BEH
Affimer molecule (A31): CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
D

E
E

H
F

C
G

F
H

I
I

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Affimer molecule (A31)

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