› 5y2m

X-ray diffraction
3.8Å resolution

Crystal structure of a group 2 HA binding antibody AF4H1K1 Fab in complex with the H4N6 duck isolate (H4-CZ/56) hemagglutinin

Released:
DOI: 10.2210/pdb5y2m/pdb
PDB entry 5y2m coloured by chain, front view.
PDB entry 5y2m coloured by chain, side view.
PDB entry 5y2m coloured by chain, top view.
Source organisms:
Entry authors: Xiao H, Qi J, Gao FG

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero hexamer (preferred)
hetero dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-107158 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Hemagglutinin Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 327 amino acids
Theoretical weight: 35.97 KDa
Source organism: Influenza A virus (A/duck/Czechoslovakia/1956(H4N6))
Expression system: Trichoplusia ni
UniProt:
  • Canonical: A3KF09 (Residues: 17-343; Coverage: 58%)
Gene name: HA
Sequence domains: Haemagglutinin
Structure domains: Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Hemagglutinin Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 176 amino acids
Theoretical weight: 20.34 KDa
Source organism: Influenza A virus (A/duck/Czechoslovakia/1956(H4N6))
Expression system: Trichoplusia ni
UniProt:
  • Canonical: A3KF09 (Residues: 344-519; Coverage: 31%)
Gene name: HA
Sequence domains: Haemagglutinin
Structure domains: Hemagglutinin Ectodomain; Chain B
a group 2 HA binding antibody AF4H1K1 Fab heavy chain Chains: I, K
Molecule details ›
Chains: I, K
Length: 233 amino acids
Theoretical weight: 24.98 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
a group 2 HA binding antibody AF4H1K1 Fab light chain Chains: J, L
Molecule details ›
Chains: J, L
Length: 220 amino acids
Theoretical weight: 24.24 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand NAG 6 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 114.175Å b: 140.94Å c: 138.1Å
α: 90° β: 95.31° γ: 90°
R-values:
R R work R free
0.238 0.236 0.277
Expression systems:
  • Trichoplusia ni
  • Homo sapiens

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