Research workbench
Ectodomain of X-31 haemagglutinin at pH 5 (state I)
Analyse Ectodomain of X-31 haemagglutinin at pH 5 (state I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y5H
- 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
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | X-31 influenza haemagglutinin HA1 | protein | 318 | 7% helix, 36% strand | P03437 |
| B, D, F | X-31 influenza haemagglutinin HA2 | protein | 172 | 51% helix, 12% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, E, B, C, D, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains E, A, C
- 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
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.86 | 0.87 | 118 | empty |
| 2 | 298 | 0.84 | 0.94 | 32 | empty |
| 3 | 338 | 0.74 | 0.86 | 30 | empty |
| 4 | 839 | 0.74 | 0.79 | 77 | empty |
| 5 | 805 | 0.74 | 0.79 | 81 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3027 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 3014 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2995 Ų buried · 30 hydrogen bonds · protein-protein
- B–F · 1495 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1478 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y5H · Ectodomain of X-31 Haemagglutinin at pH 5 (State I) · 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 6Y5H · PDBe 6Y5H · UniProt P03437
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