Research workbench
Haemagglutinin of H10N8 influenza virus isolated from humans in complex with human receptor analogue 6'SLN
Analyse Haemagglutinin of H10N8 influenza virus isolated from humans in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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