MolNFT v1 · #168467 · protein
Minimally mutated anti-influenza broadly neutralizing antibody
6WHK · Hemagglutinin HA1 chain: “Minimally mutated anti-influenza broadly neutralizing antibody”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.60). MolNFT v1 #168467 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WHK
- Type
- protein
- Length
- 644 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Fab heavy chain; Fab light chain
- UniProt
- B4UPF7
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 211 | 13% helix, 38% strand | B4UPF7 |
| C | Fab heavy chain | protein | 222 | 7% helix, 49% strand | — |
| B | Fab light chain | protein | 211 | 9% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.60 | 0.78 | 34 | empty |
| 2 | 547 | 0.60 | 0.73 | 73 | empty |
| 3 | 186 | 0.54 | 0.79 | 29 | empty |
| 4 | 80 | 0.44 | 0.80 | 14 | empty |
| 5 | 64 | 0.30 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–B · 1696 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6WHK · Minimally mutated anti-influenza broadly neutralizing antibody · 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 B4UPF7
- Elsewhere: RCSB PDB 6WHK · PDBe 6WHK · UniProt B4UPF7
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