Research workbench
Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in netherland
Analyse Crystal structure of the haemagglutinin from a transmissible H10N7 seal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TVC
- Type
- protein
- Length
- 1,473 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haemagglutinin HA1; Haemagglutinin HA2
- UniProt
- A0A0A7HR51
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Haemagglutinin HA1 | protein | 319 | 8% helix, 41% strand | A0A0A7HR51 |
| B, D, F | Haemagglutinin HA2 | protein | 172 | 54% helix, 14% strand | A0A0A7HR51 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.84 | 0.85 | 141 | empty |
| 2 | 186 | 0.83 | 0.97 | 24 | empty |
| 3 | 80 | 0.75 | 0.98 | 17 | empty |
| 4 | 80 | 0.74 | 0.97 | 17 | empty |
| 5 | 76 | 0.73 | 0.97 | 16 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3246 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 3236 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3180 Ų buried · 41 hydrogen bonds · protein-protein
- D–F · 1509 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1487 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6TVC · Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus… · 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 A0A0A7HR51
- Elsewhere: RCSB PDB 6TVC · PDBe 6TVC · UniProt A0A0A7HR51
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