MolNFT v2 · #158696 · protein
Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope
6N5B · antibody heavy chain: “Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope”. X-ray diffraction at 3.5, 1 ligand (NGA), 7 pockets (best druggability 0.64). MolNFT v2 #158696 on GenesisL1: 3D…
- PDB
- 6N5B
- Type
- protein
- Length
- 654 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Influenza A virus; Mus musculus
- Molecule
- antibody heavy chain; antibody light chain; Hemagglutinin
- Ligands
- NGA
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · resolution 3.5 · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | antibody heavy chain | protein | 222 | 7% helix, 48% strand | — |
| L | antibody light chain | protein | 211 | 8% helix, 53% strand | — |
| B | Hemagglutinin | protein | 221 | 12% helix, 36% strand | — |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains H, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.64 | 0.83 | 44 | empty |
| 2 | 514 | 0.60 | 0.74 | 51 | empty |
| 3 | 209 | 0.53 | 0.78 | 29 | empty |
| 4 | 87 | 0.37 | 0.77 | 17 | empty |
| 5 | 74 | 0.35 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1944 Ų buried · 13 hydrogen bonds · protein-protein
- H–B · 679 Ų buried · 8 hydrogen bonds · protein-protein
- L–B · 227 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, O-glycosylation).
Compared structures
- 6N5B · Broadly protective antibodies directed to a subdominant influenza hemagglutinin epitope · the same entry in another collection · chain B against B, 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 6N5B · PDBe 6N5B
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