MolNFT v1 · #88605 · protein
Haemagglutinin of H10N8 influenza virus isolated from humans in complex with human receptor analogue 6'SLN
4D00 · Haemagglutinin HA1: “Haemagglutinin of H10N8 influenza virus isolated from humans in complex with human receptor analogue 6'SLN”. X-ray diffraction, 4 ligands (NAG, GAL, SIA), 20 pockets (best druggability 0.87). MolNFT v1 #88605 on…
- PDB
- 4D00
- Type
- protein
- Length
- 1,483 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haemagglutinin HA1
- Ligands
- NAG, GAL, SIA, NI
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Haemagglutinin HA1 | protein | 319 | 9% helix, 42% strand | — |
| B | Haemagglutinin HA1 | protein | 175 | 55% helix, 13% strand | — |
| C | Haemagglutinin HA1 | protein | 321 | 9% helix, 41% strand | — |
| D | Haemagglutinin HA1 | protein | 176 | 57% helix, 13% strand | — |
| F | Haemagglutinin HA1 | protein | 173 | 58% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, D, E, F
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.87 | 0.89 | 101 | empty |
| 2 | 203 | 0.85 | 0.97 | 23 | empty |
| 3 | 219 | 0.78 | 0.92 | 27 | empty |
| 4 | 224 | 0.77 | 0.91 | 27 | empty |
| 5 | 301 | 0.77 | 0.88 | 35 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3285 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3266 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 3257 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1591 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1544 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4D00 · Haemagglutinin of H10N8 Influenza Virus Isolated from Humans in Complex with Human… · 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
- Elsewhere: RCSB PDB 4D00 · PDBe 4D00
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