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Crystal structure of influenza a virus hemagglutinin from A/OHIO/09/2015 bound to the stalk-binding CR6261 antibody Fab
Analyse Crystal structure of influenza a virus hemagglutinin from A/OHIO/09/2015 bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UYN
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; CR6261 Fab heavy chain; CR6261 Fab light chain
- UniProt
- A0A6C0TB04
- Ligands
- NAG, CL
- Pockets
- 11 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 326 | 8% helix, 39% strand | A0A6C0TB04 |
| B | Hemagglutinin HA1 chain | protein | 167 | 54% helix, 15% strand | A0A6C0TB04 |
| H | CR6261 Fab heavy chain | protein | 148 | 4% helix, 42% strand | — |
| L | CR6261 Fab light chain | protein | 149 | 7% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.46 | 0.76 | 26 | empty |
| 2 | 155 | 0.43 | 0.74 | 26 | empty |
| 3 | 50 | 0.37 | 0.80 | 20 | empty |
| 4 | 87 | 0.37 | 0.76 | 16 | empty |
| 5 | 84 | 0.37 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2783 Ų buried · 38 hydrogen bonds · protein-protein
- H–L · 1162 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 597 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 290 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6UYN · Crystal structure of influenza A virus hemagglutinin from A/Ohio/09/2015 bound to the… · 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 A0A6C0TB04
- Elsewhere: RCSB PDB 6UYN · PDBe 6UYN · UniProt A0A6C0TB04
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