SMTL ID : 8sk7.1

Cryo-EM structure of designed Influenza HA binder, HA_20, bound to Influenza HA (Strain: Iowa43)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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.1: 10 residues within 4Å: Chain A: N.64, P.65, E.66, E.86, N.87, C.90, A.134, C.135, S.136, R.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.220 NAG-NAG-BMA.3: 10 residues within 4Å: Chain D: N.64, P.65, E.66, E.86, N.87, C.90, A.134, C.135, S.136, R.220 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.220 NAG-NAG-BMA.5: 10 residues within 4Å: Chain G: N.64, P.65, E.66, E.86, N.87, C.90, A.134, C.135, S.136, R.220 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.220

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.2: 3 residues within 4Å: Chain A: T.15, N.23 Chain F: K.30 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain D: T.15, N.23 Chain I: K.30 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: K.30 Chain G: T.15, N.23 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: N.161, N.162 Chain G: E.215 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain A: N.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.11 NAG.9: 1 residues within 4Å: Chain A: N.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.268 NAG.10: 3 residues within 4Å: Chain A: D.275, T.276, N.286 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain A: E.215 Chain D: N.161, N.162 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain D: N.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.11 NAG.13: 1 residues within 4Å: Chain D: N.268 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.268 NAG.14: 3 residues within 4Å: Chain D: D.275, T.276, N.286 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain D: E.215 Chain G: N.161, N.162 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain G: N.11 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.11 NAG.17: 1 residues within 4Å: Chain G: N.268 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.268 NAG.18: 3 residues within 4Å: Chain G: D.275, T.276, N.286 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watson, J.L. et al., De novo design of protein structure and function with RFdiffusion. Nature (2023)

Release Date

2023-06-14

Peptides

Hemagglutinin HA1 chain: ADG
Hemagglutinin: BEH
HA_20 minibinder (RFdiffusion-designed): CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
G

E
H

H
I

C
X

F
Y

I
Z

Hemagglutinin HA1 chain

Hemagglutinin

HA_20 minibinder (RFdiffusion-designed)