Research workbench
Crystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in netherland in complex with human receptor analogue 6'-sln
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
- 6TVB
- Type
- protein
- Length
- 1,484 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- A0A0A7HR51
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin HA1 | protein | 320 | 9% helix, 41% strand | A0A0A7HR51 |
| B, D | Hemagglutinin HA2 | protein | 175 | 54% helix, 13% strand | A0A0A7HR51 |
| E | Hemagglutinin HA1 | protein | 322 | 9% helix, 40% strand | A0A0A7HR51 |
| F | Hemagglutinin HA2 | protein | 172 | 55% helix, 13% strand | A0A0A7HR51 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C, E, B, D
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, D, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.83 | 0.97 | 23 | empty |
| 2 | 1122 | 0.83 | 0.84 | 132 | EDO |
| 3 | 1146 | 0.76 | 0.78 | 155 | EDO |
| 4 | 76 | 0.74 | 0.97 | 16 | empty |
| 5 | 78 | 0.73 | 0.97 | 17 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3236 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3214 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 3125 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 1506 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1434 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6TVB · 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 6TVB · PDBe 6TVB · UniProt A0A0A7HR51
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