Research workbench
Extended Intermediate form of X-31 Influenza Haemagglutinin at pH 5 (State IV)
Analyse Extended Intermediate form of X-31 Influenza Haemagglutinin at pH 5 (State IV) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y5K
- Type
- protein
- Length
- 1,335 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.2
- Source
- unidentified influenza virus
- Molecule
- X-31 Influenza Haemagglutinin HA1; X-31 Influenza Haemagglutinin HA2
- UniProt
- P03437
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.69
Structure
electron microscopy · resolution 4.2 · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | X-31 Influenza Haemagglutinin HA1 | protein | 312 | 9% helix, 37% strand | P03437 |
| B, D, F | X-31 Influenza Haemagglutinin HA2 | protein | 133 | 77% helix, 5% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.69 | 0.98 | 13 | empty |
| 2 | 319 | 0.66 | 0.81 | 37 | empty |
| 3 | 181 | 0.63 | 0.84 | 35 | empty |
| 4 | 248 | 0.60 | 0.80 | 32 | empty |
| 5 | 281 | 0.60 | 0.78 | 34 | empty |
Interfaces
12 interfaces between chains.
- D–F · 1246 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1198 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 1171 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1058 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1052 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y5K · Extended intermediate form of X-31 influenza haemagglutinin at pH 5 (state IV) · 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 P03437
- Elsewhere: RCSB PDB 6Y5K · PDBe 6Y5K · UniProt P03437
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