Research workbench
BG505 sosip reconstructed from a designed nanoparticle, BG505 sosip- T33-31 (component a)
Analyse BG505 sosip reconstructed from a designed nanoparticle, BG505 sosip- T33-31… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L7T
- Type
- protein
- Length
- 1,770 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 SOSIP.V5.2(7S) - GP120; BG505 SOSIP.V5.2(7S) - GP41
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | BG505 SOSIP.V5.2(7S) - GP120 | protein | 445 | 15% helix, 42% strand | — |
| B, D, F | BG505 SOSIP.V5.2(7S) - GP41 | protein | 145 | 71% helix, 6% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, C, E, B, D, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.83 | 0.92 | 47 | empty |
| 2 | 678 | 0.75 | 0.81 | 84 | empty |
| 3 | 339 | 0.74 | 0.85 | 45 | NAG |
| 4 | 352 | 0.71 | 0.83 | 47 | NAG |
| 5 | 326 | 0.71 | 0.84 | 48 | NAG |
Interfaces
12 interfaces between chains.
- E–F · 2597 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2594 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2593 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1360 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 1355 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L7T · BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component A) · the same entry in another collection · chain D against D, 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 7L7T · PDBe 7L7T
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.