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Structure of the A_EQUINE_RICHMOND_07 H3 haemagglutinin
Analyse Structure of the A_EQUINE_RICHMOND_07 H3 haemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UO0
- Type
- protein
- Length
- 1,486 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C3TUR9
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 325 | 10% helix, 39% strand | C3TUR9 |
| B, D, F | Hemagglutinin | protein | 172 | 52% helix, 16% strand | C3TUR9 |
| C | Hemagglutinin | protein | 320 | 10% helix, 39% strand | C3TUR9 |
| E | Hemagglutinin | protein | 325 | 10% helix, 38% strand | C3TUR9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, E, B, C, D, F
- BMA · beta-D-mannopyranose · sugar · 10 copies · chains E, A, C
- MAN · alpha-D-mannopyranose · sugar · 10 copies
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B, D, F
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, F, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.86 | 0.88 | 119 | EDO |
| 2 | 295 | 0.85 | 0.96 | 33 | empty |
| 3 | 902 | 0.75 | 0.79 | 81 | empty |
| 4 | 825 | 0.75 | 0.79 | 70 | EDO |
| 5 | 516 | 0.75 | 0.83 | 62 | EDO |
Interfaces
15 interfaces between chains.
- E–F · 3098 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3043 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2992 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 1472 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1472 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 15 disulfide (N-glycosylation, disulfide).
Compared structures
- 4UO0 · Structure of the A_Equine_Richmond_07 H3 haemagglutinin · 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 C3TUR9
- Elsewhere: RCSB PDB 4UO0 · PDBe 4UO0 · UniProt C3TUR9
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