Research workbench
Crystal structure of the haemagglutinin mutant (GLN226LEU, DEL228) from an H10N7 seal influenza virus isolated in germany in complex with human receptor analogue 6'-sln
Analyse Crystal structure of the haemagglutinin mutant (GLN226LEU, DEL228) from an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TVT
- Type
- protein
- Length
- 1,452 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, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 312 | 10% helix, 41% strand | A0A0A7HR51 |
| B, D, F | Hemagglutinin HA2 | protein | 172 | 52% helix, 13% strand | A0A0A7HR51 |
| C | Hemagglutinin HA1 | protein | 311 | 9% helix, 41% strand | A0A0A7HR51 |
| E | Hemagglutinin HA1 | protein | 313 | 9% helix, 42% strand | A0A0A7HR51 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D, E, 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
- CA · Calcium ion · metal · 2 copies · chains A, B, F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.85 | 0.98 | 25 | empty |
| 2 | 1196 | 0.83 | 0.84 | 135 | empty |
| 3 | 77 | 0.73 | 0.97 | 26 | empty |
| 4 | 73 | 0.73 | 0.97 | 20 | empty |
| 5 | 77 | 0.73 | 0.96 | 17 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3314 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 3296 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 3238 Ų buried · 45 hydrogen bonds · protein-protein
- D–F · 1565 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1559 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6TVT · Crystal structure of the haemagglutinin mutant (Gln226Leu, Del228) from an H10N7 seal… · 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 6TVT · PDBe 6TVT · UniProt A0A0A7HR51
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