Research workbench
The crystal structure of hemagglutinin from A/WEDGE-tailed SHEARWATER/WESTERN AUSTRALIA/2576/1979 (H15N9)
Analyse The crystal structure of hemagglutinin from A/WEDGE-tailed SHEARWATER/WESTERN… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V49
- Type
- protein
- Length
- 1,488 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q20ND8
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 329 | 10% helix, 34% strand | Q20ND8 |
| B, D, F | Hemagglutinin HA2 chain | protein | 167 | 53% helix, 13% strand | Q20ND8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E, B, D, F
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 | 541 | 0.84 | 0.90 | 50 | empty |
| 2 | 205 | 0.83 | 0.97 | 27 | empty |
| 3 | 202 | 0.83 | 0.97 | 28 | empty |
| 4 | 206 | 0.83 | 0.96 | 27 | empty |
| 5 | 344 | 0.72 | 0.84 | 28 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3243 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 3230 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3230 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1256 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1250 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6V49 · The crystal structure of hemagglutinin from A/wedge-tailed shearwater/Western… · 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 Q20ND8
- Elsewhere: RCSB PDB 6V49 · PDBe 6V49 · UniProt Q20ND8
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