MolNFT v1 · #168820 · protein
Structural and functional analysis of a potent sarbecovirus neutralizing antibody
6WS6 · S309 antigen-binding (Fab) fragment, heavy chain: “Structural and functional analysis of a potent sarbecovirus neutralizing antibody”. X-ray diffraction, 1 ligand (JEF), 14 pockets (best druggability 0.81). MolNFT v1 #168820 on…
- PDB
- 6WS6
- Type
- protein
- Length
- 1,297 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S309 antigen-binding (Fab) fragment, heavy chain; S309 antigen-binding (Fab) fragment…
- Ligands
- JEF
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | S309 antigen-binding (Fab) fragment, heavy chain | protein | 229 | 5% helix, 51% strand | — |
| B, F | S309 antigen-binding (Fab) fragment, light chain | protein | 213 | 7% helix, 50% strand | — |
| C | S309 antigen-binding (Fab) fragment, heavy chain | protein | 212 | 6% helix, 47% strand | — |
| D | S309 antigen-binding (Fab) fragment, light chain | protein | 201 | 4% helix, 45% strand | — |
Ligands and binding sites
- JEF · O-(O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500) · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.81 | 0.82 | 130 | empty |
| 2 | 462 | 0.67 | 0.79 | 52 | empty |
| 3 | 284 | 0.63 | 0.81 | 34 | empty |
| 4 | 168 | 0.63 | 0.85 | 36 | empty |
| 5 | 466 | 0.60 | 0.75 | 54 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1853 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1848 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1504 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 1172 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6WS6 · Structural and functional analysis of a potent sarbecovirus 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
- Elsewhere: RCSB PDB 6WS6 · PDBe 6WS6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.