Research workbench
Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope
Analyse Broadly protective antibodies directed to a subdominant influenza hemagglutinin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N5D
- Type
- protein
- Length
- 2,148 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody heavy chain; Antibody light chain
- UniProt
- P03437
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K | Hemagglutinin | protein | 282 | 10% helix, 36% strand | P03437 |
| C, E, L | Antibody heavy chain | protein | 222 | 5% helix, 45% strand | — |
| N, F, D | Antibody light chain | protein | 212 | 8% helix, 50% strand | — |
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.73 | 0.77 | 90 | empty |
| 2 | 55 | 0.72 | 0.98 | 16 | empty |
| 3 | 719 | 0.66 | 0.74 | 57 | empty |
| 4 | 681 | 0.65 | 0.75 | 64 | empty |
| 5 | 526 | 0.63 | 0.75 | 67 | empty |
Interfaces
13 interfaces between chains.
- L–N · 1825 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1773 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1755 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 662 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 622 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6N5D · Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope · 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 P03437
- Elsewhere: RCSB PDB 6N5D · PDBe 6N5D · UniProt P03437
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