SMTL ID : 8tp3.1

H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1F05

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

2 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: 8 residues within 4Å: Chain A: N.81, E.83, E.103, N.104, C.107, C.152, S.153, R.237 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain E: N.81, E.83, E.103, N.104, C.107, C.152, S.153, R.237 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

NAG-NAG-BMA.2: 8 residues within 4Å: Chain C: N.81, E.83, E.103, N.104, C.107, S.153, R.237 Ligands: NAG.10 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: N.28, S.29 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: K.39, N.40 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.39 NAG.6: 1 residues within 4Å: Chain A: N.71 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: P.141, N.142, P.175 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.175 NAG.8: 5 residues within 4Å: Chain C: A.26, N.27, N.28 Chain D: T.15, V.18 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:N.27, D:V.18 NAG.9: 2 residues within 4Å: Chain C: K.39, N.40 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.39 NAG.10: 4 residues within 4Å: Chain C: G.70, N.71 Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain C: P.141, N.142 Ligands: NAG.12 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.141 NAG.12: 2 residues within 4Å: Chain C: N.176 Ligands: NAG.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.176 NAG.13: 2 residues within 4Å: Chain E: N.28, S.29 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain E: K.39, N.40 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:K.39 Hydrogen bonds: E:N.40 NAG.15: 1 residues within 4Å: Chain E: N.71 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain E: N.142, H.143, P.175, N.176 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y.R. et al., Immune memory shapes human polyclonal antibody responses to H2N2 vaccination. Biorxiv (2023)

Release Date

2023-10-11

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF
Heavy chain of Fab 1-1-1F05: G
Light chain of Fab 1-1-1F05: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
G

B
B

D
D

F
I

G
H

H
L

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Heavy chain of Fab 1-1-1F05

Light chain of Fab 1-1-1F05

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