› 8vqm

X-ray diffraction
2.21Å resolution

Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with small molecule 6R prime

Released:
DOI: 10.2210/pdb8vqm/pdb
PDB entry 8vqm coloured by chain, front view.
PDB entry 8vqm coloured by chain, side view.
PDB entry 8vqm coloured by chain, top view.
Source organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Primary publication:
Ultrapotent influenza hemagglutinin fusion inhibitors developed through SuFEx-enabled high-throughput medicinal chemistry.
Kitamura S, Lin TH, Lee CD, Takamura A, Kadam RU, Zhang D, Zhu X, Dada L, Nagai E, Yu W, Yao Y, Sharpless KB, Wilson IA, Wolan DW
Proc Natl Acad Sci U S A 121 e2310677121 (2024)
PMID: 38753503

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-272216 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Hemagglutinin HA1 chain Chain: A
Molecule details ›
Chain: A
Length: 322 amino acids
Theoretical weight: 36.16 KDa
Source organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Expression system: Spodoptera aff. frugiperda 1 BOLD-2017
UniProt:
  • Canonical: P03452 (Residues: 18-339; Coverage: 59%)
Gene name: HA
Sequence domains: Haemagglutinin
Hemagglutinin HA2 chain Chain: B
Molecule details ›
Chain: B
Length: 222 amino acids
Theoretical weight: 25.11 KDa
Source organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Expression system: Spodoptera aff. frugiperda 1 BOLD-2017
UniProt:
  • Canonical: P03452 (Residues: 344-565; Coverage: 41%)
Gene name: HA
Sequence domains: Haemagglutinin

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 1 x NAG
Ligand A1ADU 1 x A1ADU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-1
Spacegroup: I213
Unit cell:
a: 159.471Å b: 159.471Å c: 159.471Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.23
Expression system: Spodoptera aff. frugiperda 1 BOLD-2017

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