Research workbench
Crystal structure of influenza hemagglutinin (H5) in complex with a broadly neutralizing antibody F10
Analyse Crystal structure of influenza hemagglutinin (H5) in complex with a broadly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FKU
- Type
- protein
- Length
- 4,407 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Neutralizing antibody F10
- UniProt
- Q6DQ33, Q2F4V2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin | protein | 323 | 8% helix, 36% strand | Q6DQ33 |
| B, D, F | Hemagglutinin | protein | 180 | 51% helix, 12% strand | Q2F4V2 |
| H, J, L | Hemagglutinin | protein | 174 | 52% helix, 10% strand | Q2F4V2 |
| X, Y | Neutralizing antibody F10 | protein | 235 | 5% helix, 39% strand | — |
| Z | Neutralizing antibody F10 | protein | 236 | 8% helix, 40% strand | — |
| S | Neutralizing antibody F10 | protein | 233 | 1% helix, 43% strand | — |
| T, U | Neutralizing antibody F10 | protein | 234 | 4% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, C, G, E, I, K
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.85 | 0.87 | 108 | empty |
| 2 | 785 | 0.82 | 0.85 | 99 | empty |
| 3 | 335 | 0.79 | 0.89 | 65 | empty |
| 4 | 922 | 0.75 | 0.79 | 97 | empty |
| 5 | 55 | 0.72 | 0.98 | 15 | empty |
Interfaces
43 interfaces between chains.
- C–D · 2715 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2622 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2606 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 2579 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 2544 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 disulfide, 13 glycan (disulfide, N-glycosylation, glycation).
Compared structures
- 3FKU · Crystal structure of influenza hemagglutinin (H5) in complex with a broadly neutralizing… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6DQ33
- Every structure of UniProt Q2F4V2
- Elsewhere: RCSB PDB 3FKU · PDBe 3FKU · UniProt Q6DQ33 · UniProt Q2F4V2
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