MolNFT v1 · #165434 · protein
Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in netherland in complex with avian receptor analogue, 3'-sln
6TVA · Haemagglutinin HA1: “Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in…”. X-ray diffraction, 5 ligands (NAG, GAL, SIA), 20 pockets (best druggability 0.84). MolNFT v1 #165434 on…
- PDB
- 6TVA
- Type
- protein
- Length
- 1,476 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haemagglutinin HA1; Haemagglutinin HA2
- UniProt
- A0A0A7HR51
- Ligands
- NAG, GAL, SIA, MAN, BMA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Haemagglutinin HA1 | protein | 320 | 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 · 10 copies · chains A, C, D, E, B, F
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.84 | 0.86 | 143 | empty |
| 2 | 193 | 0.83 | 0.97 | 23 | empty |
| 3 | 79 | 0.75 | 0.98 | 18 | empty |
| 4 | 78 | 0.73 | 0.97 | 17 | empty |
| 5 | 75 | 0.73 | 0.97 | 18 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3269 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3188 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3182 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 1469 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1459 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6TVA · 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 6TVA · PDBe 6TVA · UniProt A0A0A7HR51
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