SMTL ID : 8tp5.1

H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1E04

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-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: 9 residues within 4Å: Chain A: N.64, E.66, E.86, N.87, C.90, S.134, C.135, S.136, R.220 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 9 residues within 4Å: Chain C: N.64, E.66, E.86, N.87, C.90, S.134, C.135, S.136, R.220 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 9 residues within 4Å: Chain G: N.64, E.66, E.86, N.87, C.90, S.134, C.135, S.136, R.220 No protein-ligand interaction detected (PLIP)

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

NAG.4: 1 residues within 4Å: Chain A: N.11 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: K.22, N.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.22 Hydrogen bonds: A:N.23 NAG.6: 1 residues within 4Å: Chain A: N.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.54 NAG.7: 2 residues within 4Å: Chain A: P.124, N.125 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.124 NAG.8: 1 residues within 4Å: Chain C: N.11 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain C: K.22, N.23 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.22 Hydrogen bonds: C:N.23 NAG.10: 1 residues within 4Å: Chain C: N.54 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.54 NAG.11: 2 residues within 4Å: Chain C: P.124, N.125 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.124 NAG.12: 1 residues within 4Å: Chain G: N.11 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain G: K.22, N.23 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:K.22 Hydrogen bonds: G:N.23 NAG.14: 1 residues within 4Å: Chain G: N.54 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.54 NAG.15: 2 residues within 4Å: Chain G: P.124, N.125 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:P.124

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: ACG
Hemagglutinin HA2 chain: BDI
Heavy chain of Fab 1-1-1E04: EHJ
Light chain of Fab 1-1-1E04: FKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

G
G

B
B

D
D

I
I

E
E

H
H

J
J

F
F

K
K

L
L

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

Heavy chain of Fab 1-1-1E04

Light chain of Fab 1-1-1E04

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