MolNFT v1 · #180686 · protein
BG505 sosip reconstructed from a designed nanoparticle, BG505 sosip- T33-31 (component B)
7L7U · BG505 SOSIP.V5.2(7S) - GP120: “BG505 sosip reconstructed from a designed nanoparticle, BG505 sosip- T33-31 (component B)”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.82). MolNFT v1 #180686 on…
- PDB
- 7L7U
- Type
- protein
- Length
- 1,761 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 0.82
Structure
electron microscopy · 2 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | BG505 SOSIP.V5.2(7S) - GP120 | protein | 442 | 15% helix, 43% strand | — |
| B, D, F | BG505 SOSIP.V5.2(7S) - GP41 | protein | 145 | 66% helix, 6% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains A, C, B, E, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.82 | 0.93 | 45 | empty |
| 2 | 1086 | 0.76 | 0.79 | 126 | empty |
| 3 | 1002 | 0.76 | 0.79 | 128 | empty |
| 4 | 363 | 0.73 | 0.84 | 53 | NAG |
| 5 | 380 | 0.72 | 0.83 | 54 | NAG |
Interfaces
15 interfaces between chains.
- C–D · 2730 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2727 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2718 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1298 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 1298 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 glycan, 24 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L7U · BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) · 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 7L7U · PDBe 7L7U
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