Research workbench
Crystal structure of the haemagglutinin from a H10N7 seal influenza virus isolated in germany in complex with human receptor analogue, 6'-sln
Analyse Crystal structure of the haemagglutinin from a H10N7 seal influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TVF
- Type
- protein
- Length
- 2,950 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- A0A0A7HR51
- Ligands
- NAG, SIA, GAL, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I | Hemagglutinin HA1 | protein | 320 | 9% helix, 41% strand | A0A0A7HR51 |
| B, D, F, H, J, L | Hemagglutinin HA2 | protein | 172 | 54% helix, 15% strand | A0A0A7HR51 |
| K | Hemagglutinin HA1 | protein | 318 | 9% helix, 41% strand | A0A0A7HR51 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, D, K, C, E, F, G, B, H, J, I, L
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, C, E, G, K, I
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, C, E, G, K
- CA · Calcium ion · metal · 3 copies · chains A, B, H, I, J, D, K, L
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 | 979 | 0.86 | 0.87 | 122 | empty |
| 2 | 206 | 0.85 | 0.97 | 23 | empty |
| 3 | 204 | 0.84 | 0.97 | 24 | empty |
| 4 | 1176 | 0.84 | 0.85 | 134 | empty |
| 5 | 82 | 0.75 | 0.98 | 17 | empty |
Interfaces
30 interfaces between chains.
- G–H · 3342 Ų buried · 40 hydrogen bonds · protein-protein
- K–L · 3332 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 3327 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 3326 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3319 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 8 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6TVF · Crystal structure of the haemagglutinin from a H10N7 seal influenza virus isolated in… · 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 6TVF · PDBe 6TVF · UniProt A0A0A7HR51
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.