MolNFT v1 · #157625 · protein
Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope
6N5E: “Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope”. X-ray diffraction, 1 ligand (NAG), 19 pockets (best druggability 0.69). MolNFT v1 #157625 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6N5E
- Type
- protein
- Length
- 2,133 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Fl-1066 heavy chain; Fl-1066 light chain
- UniProt
- P03437
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.69
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin | protein | 282 | 11% helix, 37% strand | P03437 |
| C | Hemagglutinin | protein | 277 | 11% helix, 35% strand | P03437 |
| H | Fl-1066 heavy chain | protein | 225 | 1% helix, 45% strand | — |
| E | Fl-1066 heavy chain | protein | 226 | 1% helix, 48% strand | — |
| G | Fl-1066 heavy chain | protein | 222 | 1% helix, 42% strand | — |
| I, D | Fl-1066 light chain | protein | 211 | 5% helix, 45% strand | — |
| F | Fl-1066 light chain | protein | 197 | 6% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.69 | 0.82 | 41 | empty |
| 2 | 394 | 0.66 | 0.80 | 54 | empty |
| 3 | 655 | 0.66 | 0.75 | 60 | empty |
| 4 | 645 | 0.66 | 0.75 | 59 | empty |
| 5 | 677 | 0.65 | 0.75 | 65 | empty |
Interfaces
10 interfaces between chains.
- E–D · 1836 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 1830 Ų buried · 14 hydrogen bonds · protein-protein
- G–F · 1536 Ų buried · 9 hydrogen bonds · protein-protein
- C–H · 844 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 796 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6N5E · 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 6N5E · PDBe 6N5E · UniProt P03437
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