Research workbench
Structure of H10 from human-infecting H10N8 in complex with avian receptor
Analyse Structure of H10 from human-infecting H10N8 in complex with avian receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QY1
- Type
- protein
- Length
- 5,904 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W | Hemagglutinin | protein | 318 | 8% helix, 41% strand | — |
| B, D, F, H, J, L, N, P, R, T, V, X | Hemagglutinin | protein | 174 | 56% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 31 copies · chains E, F, A, B, C, D, G, K, H, I, J, L, M, Q, N, O, P, R, S, W, T, U, V, X
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains E, G, I, U
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains E, G, I, U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.87 | 0.88 | 122 | empty |
| 2 | 1126 | 0.86 | 0.87 | 134 | empty |
| 3 | 1123 | 0.85 | 0.86 | 129 | empty |
| 4 | 212 | 0.85 | 0.97 | 24 | empty |
| 5 | 395 | 0.85 | 0.93 | 39 | empty |
Interfaces
63 interfaces between chains.
- E–F · 3235 Ų buried · 40 hydrogen bonds · protein-protein
- U–V · 3227 Ų buried · 42 hydrogen bonds · protein-protein
- O–P · 3223 Ų buried · 41 hydrogen bonds · protein-protein
- K–L · 3214 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3203 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 disulfide, 26 glycan (disulfide, N-glycosylation).
Compared structures
- 4QY1 · Structure of H10 from human-infecting H10N8 in complex with avian receptor · the same entry in another collection · chain T against T, 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 4QY1 · PDBe 4QY1
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