SMTL ID : 6wzt.1

CryoEM structure of influenza hemagglutinin A/Victoria/361/2011 in complex with cyno antibody 3B10

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.40 Å

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 2 residues within 4Å: Chain A: N.38, T.40 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.122, Q.132, N.133, N.152, R.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.122, A:R.255 NAG-NAG.7: 2 residues within 4Å: Chain D: N.38, T.40 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain D: N.122, Q.132, N.133, N.152, R.255 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.122, D:R.255 NAG-NAG.13: 2 residues within 4Å: Chain G: N.38, T.40 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain G: N.122, Q.132, N.133, N.152, R.255 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.122, G:R.255

12 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: 3 residues within 4Å: Chain A: N.45, N.285, V.297 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: E.62, N.63, Y.94 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 6 residues within 4Å: Chain A: N.165, V.166, T.167 Chain D: Y.219, R.222, N.225 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.222, D:R.222, D:N.225 NAG-NAG-BMA.6: 6 residues within 4Å: Chain A: N.165, N.246, S.247, T.248 Chain D: I.217, Y.219 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain D: N.285, V.297 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain D: E.62, N.63, Q.75, Y.94 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 8 residues within 4Å: Chain D: N.165, V.166, T.167, L.244 Chain G: Y.219, R.222, N.225 Ligands: NAG-NAG-BMA.12 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.222, G:R.222, G:R.222, G:N.225 NAG-NAG-BMA.12: 7 residues within 4Å: Chain D: A.163, R.201, N.246, S.247 Chain G: I.217, Y.219 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain G: N.45, N.285, V.297 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain G: E.62, N.63, Q.75, Y.94 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 7 residues within 4Å: Chain A: Y.219, R.222, N.225 Chain G: N.165, V.166, T.167, I.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.222, A:R.222, A:R.222, A:R.222, A:N.225 NAG-NAG-BMA.18: 5 residues within 4Å: Chain A: I.217 Chain G: N.165, R.201, N.246, T.248 No protein-ligand interaction detected (PLIP)

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

NAG.19: 3 residues within 4Å: Chain A: P.21, N.22, K.326 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.22 NAG.20: 2 residues within 4Å: Chain D: P.21, N.22 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain G: P.21, N.22 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Darricarrere, N. et al., Broad neutralization of H1 and H3 viruses by adjuvanted influenza HA stem vaccines in nonhuman primates. Sci Transl Med (2021)

Release Date

2021-03-10

Peptides

Hemagglutinin: ADG
Cyno antibody heavy chain: BEH
Cyno antibody light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
E

H
G

C
L

F
D

I
F

Hemagglutinin

Cyno antibody heavy chain

Cyno antibody light chain