Research workbench
The crystal structure of hemagglutinin from A/DUCK/MEMPHIS/546/1974 (H11N9)
Analyse The crystal structure of hemagglutinin from A/DUCK/MEMPHIS/546/1974 (H11N9) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V47
- Type
- protein
- Length
- 1,464 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q0A426, A2V851
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 321 | 8% helix, 41% strand | Q0A426 |
| B, D, F | Hemagglutinin HA2 chain | protein | 167 | 54% helix, 11% strand | A2V851 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, D, C, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.75 | 0.97 | 17 | empty |
| 2 | 991 | 0.74 | 0.77 | 107 | empty |
| 3 | 356 | 0.68 | 0.81 | 39 | empty |
| 4 | 451 | 0.64 | 0.77 | 60 | empty |
| 5 | 336 | 0.63 | 0.79 | 45 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2530 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2514 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2496 Ų buried · 31 hydrogen bonds · protein-protein
- B–F · 1097 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 1076 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6V47 · The crystal structure of hemagglutinin from A/duck/Memphis/546/1974 (H11N9) · 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 Q0A426
- Every structure of UniProt A2V851
- Elsewhere: RCSB PDB 6V47 · PDBe 6V47 · UniProt Q0A426 · UniProt A2V851
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