Research workbench
Ectodomain of X-31 haemagglutinin at pH 8
Analyse Ectodomain of X-31 haemagglutinin at pH 8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y5G
- Type
- protein
- Length
- 1,470 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- X-31 influenza haemagglutinin HA1; X-31 influenza haemagglutinin HA2
- UniProt
- P03437
- Ligands
- NAG, MAN, BMA
- Pockets
- 18 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | X-31 influenza haemagglutinin HA1 | protein | 318 | 7% helix, 38% strand | P03437 |
| B, D, F | X-31 influenza haemagglutinin HA2 | protein | 172 | 49% helix, 10% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, E, B, C, D, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains E, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.85 | 0.89 | 61 | empty |
| 2 | 347 | 0.84 | 0.93 | 34 | empty |
| 3 | 917 | 0.76 | 0.79 | 108 | empty |
| 4 | 541 | 0.76 | 0.83 | 72 | empty |
| 5 | 425 | 0.75 | 0.85 | 58 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2998 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2971 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2969 Ų buried · 26 hydrogen bonds · protein-protein
- B–F · 1438 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1430 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y5G · Ectodomain of X-31 Haemagglutinin at pH 8 · 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 6Y5G · PDBe 6Y5G · UniProt P03437
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