Research workbench
Structure of H1 influenza hemagglutinin bound to Fab 310-39G10
Analyse Structure of H1 influenza hemagglutinin bound to Fab 310-39G10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SCO
- Type
- protein
- Length
- 2,157 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; 310-39G10 Fab, heavy chain; 310-39G10…
- UniProt
- Q289M7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Hemagglutinin HA1 chain | protein | 322 | 9% helix, 41% strand | Q289M7 |
| B, D, I | Hemagglutinin HA2 chain | protein | 171 | 56% helix, 16% strand | Q289M7 |
| H, E, J | 310-39G10 Fab, heavy chain | protein | 119 | 8% helix, 52% strand | — |
| L, F, K | 310-39G10 Fab, light chain | protein | 107 | 3% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C, G, B, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.83 | 0.97 | 24 | empty |
| 2 | 678 | 0.80 | 0.85 | 84 | empty |
| 3 | 352 | 0.79 | 0.89 | 40 | empty |
| 4 | 363 | 0.78 | 0.88 | 43 | empty |
| 5 | 625 | 0.71 | 0.79 | 59 | empty |
Interfaces
30 interfaces between chains.
- A–B · 2856 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2849 Ų buried · 40 hydrogen bonds · protein-protein
- G–I · 2845 Ų buried · 40 hydrogen bonds · protein-protein
- B–I · 1038 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1024 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 7SCO · Structure of H1 influenza hemagglutinin bound to Fab 310-39G10 · 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 Q289M7
- Elsewhere: RCSB PDB 7SCO · PDBe 7SCO · UniProt Q289M7
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