Research workbench
Crystal structure of the haemagglutinin mutant (GLN226LEU, DEL228) from an H10N7 seal influenza virus isolated in germany in complex with avian receptor analogue 3'-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
- 6TXO
- Type
- protein
- Length
- 1,445 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA2; Hemagglutinin
- UniProt
- A0A0A7HR51
- Ligands
- NAG, SIA, GAL, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F | Hemagglutinin HA2 | protein | 172 | 53% helix, 13% strand | A0A0A7HR51 |
| A, E | Hemagglutinin | protein | 310 | 9% helix, 39% strand | A0A0A7HR51 |
| C | Hemagglutinin | protein | 309 | 8% helix, 41% strand | A0A0A7HR51 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, C, A, D, E, F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- CA · Calcium ion · metal · chains B, D, C
- EDO · 1,2-ethanediol · additive · chains B
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 | 1159 | 0.85 | 0.86 | 140 | empty |
| 2 | 206 | 0.84 | 0.97 | 24 | empty |
| 3 | 78 | 0.74 | 0.97 | 17 | empty |
| 4 | 89 | 0.73 | 0.96 | 26 | empty |
| 5 | 80 | 0.73 | 0.96 | 17 | empty |
Interfaces
15 interfaces between chains.
- D–C · 3309 Ų buried · 44 hydrogen bonds · protein-protein
- F–E · 3263 Ų buried · 42 hydrogen bonds · protein-protein
- B–A · 3167 Ų buried · 39 hydrogen bonds · protein-protein
- B–F · 1573 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1561 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6TXO · Crystal structure of the haemagglutinin mutant (Gln226Leu, Del228) from an H10N7 seal… · the same entry in another collection · chain B against B, 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 6TXO · PDBe 6TXO · UniProt A0A0A7HR51
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